Expand Suite ID Tool IDs Description Suite first commit date Homepage Suite version Suite conda package Latest suite conda package version Suite version status ToolShed categories EDAM operations EDAM reduced operations EDAM topics EDAM reduced topics Suite owner Suite source Suite parsed folder bio.tool ID bio.tool name bio.tool description biii ID Number of tools on UseGalaxy.org (Main) Number of tools on UseGalaxy.org.au Number of tools on UseGalaxy.eu Number of tools on UseGalaxy.fr Number of tools on APOSTL Number of tools on BioBix Number of tools on CIRM-CFBP Number of tools on ChemFlow Number of tools on Coloc-stats Number of tools on CorGAT Number of tools on CoralSNP Number of tools on CropGalaxy Number of tools on Dintor Number of tools on FreeBioinfo Number of tools on GASLINI Number of tools on Galaxy@AuBi Number of tools on Galaxy@Pasteur Number of tools on GalaxyTrakr Number of tools on Genomic Hyperbrowser Number of tools on GigaGalaxy Number of tools on IPK Galaxy Blast Suite Number of tools on ImmPort Galaxy Number of tools on InteractoMIX Number of tools on Lebanese University Galaxy Number of tools on MISSISSIPPI Number of tools on MiModD NacreousMap Number of tools on Oqtans Number of tools on Palfinder Number of tools on PepSimili Number of tools on PhagePromotor Number of tools on UseGalaxy.be Number of tools on UseGalaxy.cz Number of tools on UseGalaxy.no Number of tools on Viral Variant Visualizer (VVV) Suite users (last 5 years) (usegalaxy.eu) Suite users (usegalaxy.eu) Suite runs (last 5 years) (usegalaxy.eu) Suite runs (usegalaxy.eu) Suite users (last 5 years) (usegalaxy.org) Suite users (usegalaxy.org) Suite runs (last 5 years) (usegalaxy.org) Suite runs (usegalaxy.org) Suite users (last 5 years) (usegalaxy.org.au) Suite users (usegalaxy.org.au) Suite runs (last 5 years) (usegalaxy.org.au) Suite runs (usegalaxy.org.au) Suite users (last 5 years) (usegalaxy.fr) Suite users (usegalaxy.fr) Suite runs (last 5 years) (usegalaxy.fr) Suite runs (usegalaxy.fr) Suite users (last 5 years) on main servers Suite users on main servers Suite runs (last 5 years) on main servers Suite runs on main servers Related Workflows Related Tutorials
2d_auto_threshold ip_threshold Automatic thresholding 2019-01-22 https://github.com/bmcv 0.25.0 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 106 125 1275 6826 2 2 11 11 12 12 440 440 0 0 0 0 120 379 1726 10729 https://dev.workflowhub.eu/workflows/1258?version=3, https://dev.workflowhub.eu/workflows/1270?version=3, https://dev.workflowhub.eu/workflows/1364?version=1, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.eu/published/workflow?id=e87e726b57f1a875, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/parameter-tuning, imaging/process-image-bioimageio, imaging/voronoi-segmentation
2d_feature_extraction ip_2d_feature_extraction 2D feature extraction 2019-01-08 https://github.com/bmcv 0.18.1 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 44 819 13885 0 0 0 0 4 4 142 142 0 0 0 0 34 116 961 15949 https://dev.workflowhub.eu/workflows/1270?version=3, https://dev.workflowhub.eu/workflows/1364?version=1, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8, https://workflowhub.eu/workflows/1259?version=1 imaging/hela-screen-analysis, imaging/voronoi-segmentation
2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules 2019-07-19 https://github.com/bmcv 0.0.1-4 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 40 407 6875 0 0 0 0 3 3 140 140 0 0 0 0 29 101 547 8109 https://dev.workflowhub.eu/workflows/1270?version=3, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8 imaging/hela-screen-analysis
2d_histogram_equalization ip_histogram_equalization 2d histogram equalization 2019-07-23 https://github.com/bmcv 0.18.1 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 103 740 807 2 2 6 6 15 15 258 258 0 0 0 0 102 324 1004 3079 https://dev.workflowhub.eu/workflows/1258?version=3, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/2D-spot-detection, imaging/imaging-introduction, imaging/parameter-tuning
2d_simple_filter ip_filter_standard 2d simple filter 2019-01-22 https://github.com/bmcv 1.12.0 scipy To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter scipy 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 83 103 751 6302 2 2 3 3 15 15 307 307 0 0 0 0 100 320 1061 8734 https://dev.workflowhub.eu/workflows/1258?version=3, https://dev.workflowhub.eu/workflows/1270?version=3, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/parameter-tuning, imaging/voronoi-segmentation
2dnmrannotation 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra 2020-02-04 http://workflow4metabolomics.org 2.0.0+galaxy2 r-batch 1.1_4 To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 57 57 12 36 57 171
Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. 2015-10-02 https://rest.ensembl.org 1.0.0 python To update Data Source earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/main/tools/Ensembl-REST 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 129 168 417 2927 0 0 0 0 0 0 0 0 0 0 0 0 129 426 417 3761 https://usegalaxy.eu/published/workflow?id=d22dac11eba8c5a3
abacas abacas Order and Orientate Contigs 2019-11-20 https://github.com/phac-nml/abacas 1.1 mummer 3.23 To update Assembly nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
anisotropic_diffusion ip_anisotropic_diffusion Anisotropic image diffusion 2018-12-04 https://github.com/bmcv 0.4.0 medpy 0.4.0 Up-to-date Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 2 26 41 0 0 0 0 0 0 0 0 0 0 0 0 2 6 26 93
apoc apoc Large-scale structural comparison of protein pockets 2017-07-04 https://sites.gatech.edu/cssb/apoc/ 1.0+galaxy1 apoc 1b16 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/apoc 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 5 8 8 1 1 1 1 0 0 0 0 0 0 0 0 6 18 9 27
apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy 2017-06-12 https://github.com/galaxy-genome-annotation/python-apollo apollo 4.2.13 To update Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 0 1061 1110 4512 4820 4 4 6 6 0 0 0 0 0 0 0 0 1065 3244 4518 13862 https://dev.workflowhub.eu/workflows/1190?version=2, https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6, https://workflowhub.eu/workflows/749?version=1 genome-annotation/apollo, genome-annotation/apollo-euk
askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ 2017-08-11 https://github.com/askomics/ askocli 0.5 To update Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
askor_de askor_de AskoR links EdgeR and AskOmics 2018-04-06 https://github.com/askomics/askoR 0.2 bioconductor-limma 3.62.1 To update Transcriptomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 3 3 1 3 3 9
assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) 2017-10-13 https://github.com/phac-nml/galaxy_tools 1.1.0 perl-bioperl 1.7.8 To update Assembly nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
background_removal background_removal Background removal filters using scikit-image 2024-07-12 https://github.com/bmcv 0.24.0 scikit-image To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tools/background_removal https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 30 30 0 0 0 0 0 0 0 0 0 0 0 0 3 9 30 90
bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. 2017-10-13 https://github.com/phac-nml/galaxy_tools 1.1.0 perl To update Assembly nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. 2020-04-28 https://github.com/tommyau/bamclipper 1.0.0 bamclipper 1.0.0 Up-to-date Sequence Analysis nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. 2022-03-03 https://www.cesgo.org/catibaric/ 1.1.0 To update Data Source genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 16 16 5 15 16 48
batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs 2024-04-30 https://github.com/galaxyproject/KegAlign 1.04.22 lastz 1.04.52 To update Next Gen Mappers richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 23 226 226 0 0 0 0 0 0 0 0 23 69 226 678 https://usegalaxy.org/published/workflow?id=ca68ad0d7420c615
bfconvert ip_convertimage Convert image 2019-07-22 https://github.com/bmcv 6.7.0 bftools 8.0.0 To update Imaging, Convert Formats imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert python-bioformats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 126 1601 1713 1 1 1 1 23 23 404 404 0 0 0 0 131 412 2006 6130 https://dev.workflowhub.eu/workflows/1267?version=2, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/multiplex-tissue-imaging-TMA, imaging/voronoi-segmentation
binary2labelimage ip_binary_to_labelimage Binary 2 label image 2017-02-11 https://github.com/bmcv 0.6 giatools 0.4.1 To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 91 432 1446 3 3 5 5 10 10 238 238 0 0 0 0 88 280 675 3039 https://dev.workflowhub.eu/workflows/1258?version=3, https://dev.workflowhub.eu/workflows/1270?version=3, https://dev.workflowhub.eu/workflows/1364?version=1, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/2D-spot-detection, imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/process-image-bioimageio, imaging/voronoi-segmentation
binaryimage2points ip_binaryimage_to_points Binary Image to Points 2017-10-30 https://github.com/bmcv 0.1-2 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 1 17 29 0 0 0 0 0 0 0 0 0 0 0 0 1 3 17 63
bioformats2raw bf2raw Convert image to OME-Zarr 2023-11-02 https://github.com/Euro-BioImaging 0.7.0 To update Imaging, Convert Formats imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 62 62 0 0 0 0 0 0 0 0 0 0 0 0 4 12 62 186
biohansel biohansel Heidelberg and Enteritidis SNP Elucidation 2018-08-01 https://github.com/phac-nml/biohansel 2.4.0 bio_hansel 2.6.1 To update Sequence Analysis nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form 2019-03-15 https://github.com/phac-nml/galaxy_tools 0.2.0 pandas To update Text Manipulation nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blast_parser blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input 2015-08-06 https://github.com/TGAC/earlham-galaxytools/ 0.2.0 python To update Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/main/tools/blast_parser 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 111 119 518 563 0 0 0 0 0 0 0 0 0 0 0 0 111 341 518 1599 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
braker braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . 2021-10-05 https://github.com/Gaius-Augustus/BRAKER 2.1.6 To update Genome annotation genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 66 66 208 208 0 0 0 0 0 0 0 0 1 1 9 9 67 201 217 651
braker3 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . 2023-06-13 https://github.com/Gaius-Augustus/BRAKER 3.0.8 To update Genome annotation Genome annotation, Gene prediction Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis RNA-Seq, Genomics, Structure prediction, Sequence analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 447 447 3164 3164 0 0 0 0 91 91 561 561 17 17 203 203 555 1665 3928 11784 genome-annotation/braker3
bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download 2015-11-20 1.3.0 perl-getopt-long 2.58 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 78 83 1659 1707 36 36 1891 1891 115 350 3552 10704 https://workflowhub.eu/workflows/373?version=2, https://workflowhub.eu/workflows/374?version=1, https://workflowhub.eu/workflows/375?version=1
camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos, CAMERA_findAdducts, CAMERA_findIsotopes, CAMERA_groupCorr, CAMERA_groupFWHM 2023-05-25 1.48.0 r-snow 0.4_1 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1 2 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 129 142 642 818 39 39 80 80 25 26 747 822 893 893 14789 14795 1086 3272 16258 49031 https://dev.workflowhub.eu/workflows/1065?version=1, https://usegalaxy.fr/published/workflow?id=06fa7dd6eea42350, https://usegalaxy.fr/published/workflow?id=15275ba7c23028ed, https://usegalaxy.fr/published/workflow?id=180744a2f8dca6eb, https://usegalaxy.fr/published/workflow?id=19e99a5c09c01bb7, https://usegalaxy.fr/published/workflow?id=26a3e5741d66982a, https://usegalaxy.fr/published/workflow?id=26bdb32c017d798c, https://usegalaxy.fr/published/workflow?id=2ee479308227a926, https://usegalaxy.fr/published/workflow?id=3c41c4c5a6332c25, https://usegalaxy.fr/published/workflow?id=57748aa2cecf0405, https://usegalaxy.fr/published/workflow?id=5964606a3836cbdf, https://usegalaxy.fr/published/workflow?id=5ec8a143f82a8c90, https://usegalaxy.fr/published/workflow?id=6895bf9cff915ba1, https://usegalaxy.fr/published/workflow?id=7a790b0acf8ba14d, https://usegalaxy.fr/published/workflow?id=7cc77d6cdd8de027, https://usegalaxy.fr/published/workflow?id=98bb6a831a2b399d, https://usegalaxy.fr/published/workflow?id=b6311795ae10032b, https://usegalaxy.fr/published/workflow?id=bb69fa998b900cb8, https://usegalaxy.fr/published/workflow?id=bcd348178335a19b, https://usegalaxy.fr/published/workflow?id=dc17a87057dec748, https://usegalaxy.fr/published/workflow?id=e6a55d00f1364794, https://usegalaxy.fr/published/workflow?id=e6f26a543c3e044a, https://usegalaxy.fr/published/workflow?id=f49e102f63d3e2bb, https://usegalaxy.org.au/published/workflow?id=f9e5caaf08a450ec, https://usegalaxy.org.au/published/workflow?id=fa0243ff9b5ca997, https://usegalaxy.org/published/workflow?id=aeeaf3e06a13bc22, https://workflowhub.eu/workflows/677?version=1 metabolomics/lcms, metabolomics/lcms-preprocessing
cfmid cfmid Competitive Fragmentation Modeling (CFM) 2019-03-07 https://sourceforge.net/p/cfm-id/ 33 cfm 33 Up-to-date Metabolomics computational-metabolomics https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado 2018-06-11 https://github.com/galaxy-genome-annotation/python-chado python-chado 2.3.9 To update Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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galaxy-interface/collections, galaxy-interface/workflow-automation, genome-annotation/gene-centric, genome-annotation/secondary-metabolite-discovery, imaging/hela-screen-analysis, imaging/parameter-tuning, introduction/galaxy-intro-ngs-data-managment, microbiome/clinical-mp-3-verification, microbiome/mothur-miseq-sop-short, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-3-verification, proteomics/neoantigen-3-fragpipe-discovery, single-cell/bulk-deconvolution-evaluate, variant-analysis/aiv-analysis, variant-analysis/baculovirus-isolate-variation
color_deconvolution ip_color_deconvolution Color-deconvolution methods 2024-09-30 https://github.com/bmcv 0.9 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 4 5 44 45 0 0 0 0 0 0 0 0 0 0 0 0 4 13 44 133
colorize_labels colorize_labels Colorize label map 2024-03-12 https://github.com/bmcv 3.2.1 networkx To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 62 62 0 0 0 0 0 0 0 0 0 0 0 0 5 15 62 186 https://dev.workflowhub.eu/workflows/1364?version=1 imaging/voronoi-segmentation
combine_assemblystats combine_stats Combine multiple Assemblystats datasets into a single tabular report 2017-11-08 https://github.com/phac-nml/galaxy_tools 1.0 perl-getopt-long 2.58 To update Assembly nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
combine_json combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. 2018-03-02 0.1 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
combine_tabular_collection combine Combine Tabular Collection into a single file 2017-02-06 0.1 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
concat_channels ip_concat_channels Concatenate images 2017-10-30 https://github.com/bmcv 0.3-1 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 12 13 68 84 0 0 0 0 0 0 0 0 0 0 0 0 12 37 68 220
concat_paired concat_fastqs Concatenate paired datasets 2019-12-16 https://github.com/phac-nml/concat 0.2 To update Text Manipulation nml https://github.com/phac-nml/concat https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI 2019-01-08 https://github.com/bmcv 0.0.4-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11 11 15589 16547 0 0 0 0 0 0 0 0 0 0 0 0 11 33 15589 47725 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc
correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis 2020-12-08 http://workflow4metabolomics.org 1.0.1+galaxy2 r-batch 1.1_4 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 55 231 231 55 165 231 693
count_objects ip_count_objects Count Objects 2019-01-08 https://github.com/bmcv 0.0.5-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 76 300 341 3 3 4 4 7 7 158 158 0 0 0 0 72 230 462 1427 https://dev.workflowhub.eu/workflows/1258?version=3, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/771?version=2 imaging/imaging-introduction, imaging/voronoi-segmentation
crop_image ip_crop_image Crop image 2025-06-06 https://github.com/bmcv 0.4.1 giatools 0.4.1 Up-to-date Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image giatools giatools Tools required for Galaxy Image Analysis 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cryptogenotyper CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. 2020-10-14 https://github.com/phac-nml/CryptoGenotyper 1.0 cryptogenotyper 1.0 Up-to-date Sequence Analysis nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 28 28 11902 11902 0 0 0 0 0 0 0 0 0 0 0 0 28 84 11902 35706
csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files 2019-08-23 https://bioinf.shenwei.me/csvtk/ 0.20.0 csvtk 0.31.0 To update Text Manipulation nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0 6 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 124 124 17 51 124 372
curve_fitting ip_curve_fitting Polynomial curve fitting to data points 2021-07-22 https://github.com/BMCV/galaxy-image-analysis 0.0.3-2 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 29 29 0 0 0 0 0 0 0 0 0 0 0 0 3 9 29 87 https://dev.workflowhub.eu/workflows/1374?version=1, https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2 imaging/detection-of-mitoflashes
detection_viz ip_detection_viz Detection Visualization 2017-10-30 https://github.com/bmcv 0.3-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9 9 34 49 0 0 0 0 0 0 0 0 0 0 0 0 9 27 34 117
ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species 2018-12-21 https://github.com/phac-nml/ecoli_serotyping 2.0.0 ectyper 2.0.0 Up-to-date Sequence Analysis Sequence assembly, Read pre-processing, Variant calling Sequence assembly, Read pre-processing, Variant calling Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper ectyper ECTyper Ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats. (Galaxy Version 1.0.0) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 163 163 16569 16569 1 1 10 10 0 0 0 0 0 0 0 0 164 492 16579 49737
ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit 2016-06-01 https://etetoolkit.org/ 3.1.3 ete3 3.1.1 To update Phylogenetics Phylogenetic analysis, Phylogenetic tree editing Phylogenetic tree editing Phylogenetics Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 0 86 111 674 976 0 0 0 0 0 0 0 0 3 3 9 9 89 292 683 2351
export_to_cluster export_to_cluster Export datasets to cluster 2016-01-18 https://github.com/TGAC/earlham-galaxytools/ 0.1.0 python To update Data Export earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/export_to_cluster 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format 2017-10-11 https://github.com/phac-nml/galaxy_tools 1.0.0 perl-bioperl 1.7.8 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fasta_extract fa-extract-sequence extract single fasta from multiple fasta file 2016-10-26 https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract 1.1.0 perl-bioperl 1.7.8 To update Sequence Analysis nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 10 0 0 0 0 134 181 1222 1827 0 0 0 0 134 450 1222 4281
fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report 2017-10-11 https://github.com/phac-nml/galaxy_tools 1.2 perl-bioperl 1.7.8 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 2018-04-11 https://github.com/tderrien/FEELnc 0.1 perl-bioperl 1.7.8 To update Convert Formats genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
feht feht Automatically identify makers predictive of groups. 2017-10-11 https://github.com/phac-nml/galaxy_tools 0.1.0 feht 1.1.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds 2017-10-12 https://github.com/phac-nml/galaxy_tools/ 1.0.1 perl-bioperl 1.7.8 To update Assembly nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gafa gafa Gene Align and Family Aggregator 2016-12-15 https://github.com/TGAC/Aequatus 0.4.1 python To update Visualization earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/GAFA 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 6 30 47 0 0 0 0 0 0 0 0 0 0 0 0 5 16 30 107 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
gblocks gblocks Gblocks 2018-04-11 https://www.biologiaevolutiva.org/jcastresana/Gblocks/Gblocks_documentation.html 0.91b gblocks 0.91b Up-to-date Sequence Analysis earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gblocks 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 80 80 561 561 4 4 19 19 84 252 580 1740
gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor 2021-09-16 0.1.0 openjdk To update Metabolomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs 2023-03-15 https://github.com/p2m2/p2m2tools 0.2.1 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io 2021-09-17 https://genenotebook.github.io 0.4.16 genoboo 0.4.16 Up-to-date Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 7 7 0 0 0 0 0 0 0 0 6 6 288 288 9 27 295 885
genform genform genform: generation of molecular formulas by high-resolution MS and MS/MS data 2019-09-12 https://sourceforge.net/projects/genform/ genform r8 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3 4 50 68 0 0 0 0 0 0 0 0 0 0 0 0 3 10 50 168
get_pairs get_pairs Separate paired and unpaired reads from two fastq files 2018-09-10 0.3 python To update Fastq Manipulation genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
getmlst getmlst Download MLST datasets by species from pubmlst.org 2015-12-03 0.1.4.1 srst2 0.2.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gnali gnali A tool to find nonessential, loss-of-function gene variants 2020-03-30 https://github.com/phac-nml/gnali/ 1.1.0 gnali 1.1.0 Up-to-date Variant Analysis nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gstf_preparation gstf_preparation GeneSeqToFamily preparation converts data for the workflow 2017-03-15 https://github.com/TGAC/earlham-galaxytools/ 0.4.3 python To update Convert Formats earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gstf_preparation 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 17 18 288 401 0 0 0 0 0 0 0 0 0 0 0 0 17 52 288 977
hcluster_sg hcluster_sg Hierarchically clustering on a sparse graph 2015-08-05 https://github.com/douglasgscofield/hcluster 0.5.1.1 hcluster_sg 0.5.1 To update Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 54 61 246 287 0 0 0 0 0 0 0 0 0 0 0 0 54 169 246 779 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
hcluster_sg_parser hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids 2015-08-12 https://github.com/TGAC/earlham-galaxytools/ 0.3.0 python To update Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg_parser 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 21 26 242 297 0 0 0 0 0 0 0 0 0 0 0 0 21 68 242 781 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
helixer helixer Gene calling with Deep Neural Networks 2023-06-14 https://github.com/weberlab-hhu/Helixer 0.3.3 To update Genome annotation Gene prediction, Genome annotation Gene prediction, Genome annotation Sequence analysis, Gene transcripts Sequence analysis, Gene transcripts genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer helixer Helixer Deep Learning to predict gene annotations 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 461 461 15 15 44 44 43 43 240 240 11 11 268 268 161 483 1013 3039 https://dev.workflowhub.eu/workflows/1358?version=2, https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=7de6e20699183cd3, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.eu/published/workflow?id=9fb31a16b258cc1a, https://usegalaxy.fr/published/workflow?id=2c823ac083c3cb6d, https://usegalaxy.fr/published/workflow?id=55be36ab73515e65, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://workflowhub.eu/workflows/1255?version=2 genome-annotation/helixer
hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. 2015-12-10 1.0.1 hivtrace 1.5.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
image_info ip_imageinfo Extracts image metadata 2019-07-19 https://github.com/bmcv 5.7.1 bftools 8.0.0 To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info python-bioformats 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 88 106 242 667 0 0 0 0 16 16 180 180 0 0 0 0 104 330 422 1691 https://dev.workflowhub.eu/workflows/1258?version=3, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed imaging/imaging-introduction, imaging/voronoi-segmentation
image_math image_math Process images using arithmetic expressions 2024-03-09 https://github.com/bmcv 1.26.4 numpy To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 74 74 0 0 0 0 0 0 0 0 0 0 0 0 3 9 74 222 imaging/process-image-bioimageio, imaging/voronoi-segmentation
image_registration_affine ip_image_registration Intensity-based Image Registration 2020-12-29 https://github.com/bmcv 0.0.3-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 16 16 0 0 0 0 0 0 0 0 0 0 0 0 5 15 16 48
imagecoordinates_flipaxis imagecoordinates_flipaxis Flip coordinate axes 2019-03-08 https://github.com/bmcv 0.1-2 pandas To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10 12 20930 21850 0 0 0 0 0 0 0 0 0 0 0 0 10 32 20930 63710 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc
influx_si influx_si metabolic flux estimation based on [in]stationary labeling 2020-04-17 https://github.com/sgsokol/influx 7.0.1 influx_si 7.3.0 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 18 18 2 6 18 54 https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac
influx_si_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows 2024-02-09 https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ 1.0.2 influx-si-data-manager 1.0.3 To update Metabolomics workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 9 9 1 3 9 27 https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac
ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO 2019-10-02 https://github.com/rietho/IPO 1.10.0 bioconductor-ipo 1.32.0 To update Metabolomics lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
isoplot isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments 2021-07-12 https://github.com/llegregam/Isoplot 1.3.1 jinja2 To update Metabolomics, Visualization workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 5 5 0 0 0 0 0 0 0 0 11 11 132 132 14 42 137 411 https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac
jbrowse_to_container jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container 2016-11-08 https://jbrowse.org python To update Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. 2017-04-10 0.3.0 kaptive 3.1.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes 2017-03-13 2.3 kat 2.4.2 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. 2017-02-06 2.3 kat 2.4.2 To update nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kegalign kegalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. 2024-08-29 https://github.com/galaxyproject/KegAlign 0.1.2.7 kegalign-full 0.1.2.7 Up-to-date Next Gen Mappers richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 138 138 0 0 0 0 0 0 0 0 31 93 138 414 https://usegalaxy.org/published/workflow?id=ca68ad0d7420c615
kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file 2023-07-10 https://github.com/workflow4metabolomics/tools-metabolomics 1.0.0 click To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
label_to_binary label_to_binary Convert label map to binary image 2024-03-13 https://github.com/bmcv 1.26.4 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
labelimage2points ip_labelimage_to_points Label Image to Points 2017-10-30 https://github.com/bmcv 0.2-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 2 25 38 0 0 0 0 0 0 0 0 0 0 0 0 2 6 25 88
landmark_registration ip_landmark_registration Landmark Registration 2019-02-04 https://github.com/bmcv 0.1.0-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 14 16 859 931 4 4 5 5 0 0 0 0 0 0 0 0 18 56 864 2664 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=1eaff95bfeb13890, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc
logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence 2018-06-06 http://logol.genouest.org/web/app.php/logol 1.7.8 logol 1.7.8 Up-to-date Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lotus2 lotus2 LotuS2 OTU processing pipeline 2021-05-13 https://lotus2.earlham.ac.uk/ 2.32 lotus2 2.34.1 To update Metagenomics Sequence feature detection, DNA barcoding Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology Metagenomics, Taxonomy, Microbial ecology earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/main/tools/lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 202 202 1566 1566 0 0 0 0 14 14 181 181 0 0 0 0 216 648 1747 5241 https://dev.workflowhub.eu/workflows/1366?version=1, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 microbiome/lotus2-identifying-fungi
mahotas_features ip_mahotas_features Compute image features using mahotas. 2024-09-30 https://github.com/luispedro/mahotas 0.7-2 mahotas To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features mahotas-feature-computation 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 6 6 32 44 0 0 0 0 0 0 0 0 0 0 0 0 6 18 32 108
mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome 2019-11-19 https://github.com/phac-nml/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 To update Sequence Analysis nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network 2018-06-11 http://bioasp.github.io/meneco/ 1.5.2 meneco 1.5.2 Up-to-date Systems Biology genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Label Image 2019-01-08 https://github.com/bmcv 0.3-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 3 11 25 0 0 0 0 0 0 0 0 0 0 0 0 2 7 11 47
metfrag metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) 2018-03-25 https://github.com/computational-metabolomics/metfrag-galaxy 2.4.5+galaxy3 metfrag 2.4.5 To update Metabolomics computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 21 21 199 199 0 0 0 0 0 0 0 0 73 73 391 391 94 282 590 1770 https://usegalaxy.fr/published/workflow?id=bcd348178335a19b
metfrag-vis metfrag_vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag 2020-06-30 https://github.com/computational-metabolomics/metfrag-galaxy 2.4.5+galaxy0 metfrag 2.4.5 To update Metabolomics computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14 14 52 52 0 0 0 0 0 0 0 0 0 0 0 0 14 42 52 156
miranda miranda Finds potential target sites for miRNAs in genomic sequences 2015-10-30 https://github.com/hacktrackgnulinux/miranda 3.3a+galaxy1 miranda 3.3a To update RNA earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/main/tools/miranda 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 105 6691 7072 0 0 0 0 0 0 0 0 23 23 27 27 116 360 6718 20535
miranda2asko miranda2asko Converts miRanda output into AskOmics format 2018-04-12 0.2 perl To update Convert Formats genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mixmodel4repeated_measures mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model 2022-05-16 http://workflow4metabolomics.org 3.1.0+galaxy1 r-lme4 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 33 305 305 33 99 305 915
mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies 2018-04-30 https://github.com/phac-nml/mob-suite 3.1.9 mob_suite 3.1.9 Up-to-date Sequence Analysis Clustering, Sequence analysis Clustering, Sequence analysis Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements, Genomics Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite mob_suite mob_suite MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assembliesThe MOB-suite depends on a series of databases which are too large to be hosted in git-hub. They can be downloaded or updated by running mob_init or if running any of the tools for the first time, the databases will download and initialize automatically if you do not specify an alternate database location. 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 824 824 147109 147109 2 2 42 42 262 262 46372 46372 16 16 46 46 1104 3312 193569 580707 https://workflowhub.eu/workflows/407?version=1
morphological_operations morphological_operations Apply morphological operations to images 2024-03-08 https://github.com/bmcv 1.12.0 scipy To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations scipy 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mrbayes mrbayes A program for the Bayesian estimation of phylogeny. 2015-12-04 1.0.2 mrbayes 3.2.7 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. 2022-03-15 http://workflow4metabolomics.org 2.2.1 r-base To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 157 157 10 30 157 471
msPurity mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data 2019-05-24 https://github.com/computational-metabolomics/mspurity-galaxy 1.28.0 bioconductor-mspurity 1.32.0 To update Metabolomics computational-metabolomics https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity 0 0 10 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 105 105 869 869 0 0 0 0 0 0 0 0 773 773 10771 10771 878 2634 11640 34920 https://usegalaxy.fr/published/workflow?id=6babfa7409467035, https://usegalaxy.fr/published/workflow?id=bcd348178335a19b, https://usegalaxy.fr/published/workflow?id=cca13353d553319e
msp_split msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data 2019-09-24 https://github.com/computational-metabolomics/mspurity-galaxy 0.0.2 To update Metabolomics tomnl https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. 2018-09-28 https://github.com/phac-nml/mykrobe-parser 0.1.4.1 r-base To update Sequence Analysis nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mzxmlshaper mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML 2024-09-20 https://rdrr.io/bioc/mzR/ 1.0.0+galaxy1 r-base To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 502 502 3 9 502 1506
ncbi_egapx ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) 2024-08-19 https://github.com/ncbi/egapx 0.3.2-alpha To update Genome annotation richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 515 515 0 0 0 0 0 0 0 0 26 78 515 1545 https://usegalaxy.org/published/workflow?id=951575e9a352301c, https://usegalaxy.org/published/workflow?id=ce488732866ba48f, https://usegalaxy.org/published/workflow?id=e93a0522ec3a35e6
ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. 2024-02-23 https://github.com/ncbi/fcs 0.5.0 To update Sequence Analysis richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 3 3 207 207 2152 2152 0 0 0 0 0 0 0 0 208 624 2155 6465 sequence-analysis/ncbi-fcs
nmr_annotation NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation 2019-07-30 http://workflow4metabolomics.org 3.0.0+galaxy1 libgfortran To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 5 40 50 0 0 0 0 0 0 0 0 47 47 373 373 52 156 413 1249
nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction 2019-07-29 http://workflow4metabolomics.org r-batch 1.1_4 To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 8 8 126 142 0 0 0 0 9 9 343 379 169 169 2225 2225 186 558 2694 8134
normalization normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data 2019-07-30 http://workflow4metabolomics.org 1.0.7+galaxy2 r-batch 1.1_4 To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 47 48 191 211 0 0 0 0 12 13 237 256 306 306 2977 2977 365 1097 3405 10254 https://usegalaxy.eu/published/workflow?id=3e2718f1ba1a22be metabolomics/lcms-dataprocessing
openlabcds2csv openlabcds2csv Creates a summary of several "Internal Standard Report" OpenLabCDS results. 2021-10-28 0.1.0 openjdk To update Metabolomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
orientationpy orientationpy Compute image orientation 2024-03-12 https://github.com/bmcv 0.2.0.4 orientationpy 0.2.0.4 Up-to-date Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy orientationj 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
overlay_images ip_overlay_images Overlay two images 2022-02-26 https://github.com/BMCV/galaxy-image-analysis 0.0.4 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 34 34 187 187 1 1 1 1 2 2 152 152 0 0 0 0 37 111 340 1020 https://dev.workflowhub.eu/workflows/1258?version=3, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/771?version=2 imaging/2D-spot-detection, imaging/imaging-introduction, imaging/process-image-bioimageio, imaging/voronoi-segmentation
pangolin pangolin Phylogenetic Assignment of Named Global Outbreak LINeages 2020-05-01 https://github.com/hCoV-2019/pangolin 1.1.14 pangolin 4.3.1 To update Sequence Analysis nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 573 573 7622 7622 391 391 8560 8560 268 268 2952 2952 12 12 548 548 1244 3732 19682 59046 https://dev.workflowhub.eu/workflows/1293?version=1, https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=5c15f251642bfa1f, https://usegalaxy.eu/published/workflow?id=74f19aff1b9cdd6b, https://usegalaxy.eu/published/workflow?id=9feebfc6c34da287, https://usegalaxy.fr/published/workflow?id=2345fad7dac13daa, https://usegalaxy.fr/published/workflow?id=591c57173e259ca6, https://usegalaxy.fr/published/workflow?id=e4735d214a68b790, https://usegalaxy.fr/published/workflow?id=feb57548b3ce914d, https://usegalaxy.org.au/published/workflow?id=7563b3ef697a69fd, https://usegalaxy.org/published/workflow?id=0fa2ce12c2874b1d, https://usegalaxy.org/published/workflow?id=4b41a8247f52c463, https://usegalaxy.org/published/workflow?id=8b81b9a3b49bbf98, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://workflowhub.eu/workflows/155?version=5 galaxy-interface/workflow-automation, variant-analysis/sars-cov-2-variant-discovery
patrist patrist Extract Patristic Distance From a Tree 2019-12-14 https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 0.1.2 python To update Phylogenetics nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes 2021-11-03 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 2.1 To update Proteomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 6 6 1 3 6 18
permutate_axis ip_permutate_axis Permutates axes 2017-10-30 https://github.com/bmcv 0.2-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 2 26 42 0 0 0 0 0 0 0 0 0 0 0 0 1 4 26 94
physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes 2022-09-26 physiofit.readthedocs.io 3.4.0 physiofit 3.4.0 Up-to-date Metabolomics workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 28 28 2 6 28 84 https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac
physiofit_manager physiofit_data_manager Handling of physiofit input files 2022-11-03 physiofit.readthedocs.io 1.0.1 physiofit_data_manager 1.0.1 Up-to-date Metabolomics workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 9 9 1 3 9 27 https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac
plantseg plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images 2024-06-19 https://github.com/bmcv 1.8.1 plant-seg To update Imaging Network analysis, Quantification, Microscope image visualisation Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg plantseg PlantSeg Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plasmid_profiler plasmid_profiler Explores plasmid content in WGS data 2016-11-07 0.1.6 r To update nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plasmidspades plasmidspades Genome assembler for assemblying plasmid 2016-06-06 1.1 spades 4.2.0 To update Assembly nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plotheatmap plotheatmap Plot heatmap of gene expression data 2017-07-04 https://github.com/TGAC/earlham-galaxytools/ 1.0 bioconductor-preprocesscore 1.68.0 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads 2020-03-24 https://github.com/phe-bioinformatics/PneumoCaT 1.2.1 pneumocat 1.2.1 Up-to-date Variant Analysis nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
points2labelimage ip_points_to_label Points to label image 2017-10-30 https://github.com/bmcv 0.4.1 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 2 46 54 0 0 0 0 0 0 0 0 0 0 0 0 2 6 46 146 imaging/2D-spot-detection
points_association_nn ip_points_association_nn Association of points in consecutive frames 2021-07-22 https://github.com/BMCV/galaxy-image-analysis 0.0.3-2 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 46 46 0 0 0 0 0 0 0 0 0 0 0 0 5 15 46 138 https://dev.workflowhub.eu/workflows/1374?version=1, https://usegalaxy.eu/published/workflow?id=e25f3ca3a1b4e4d8, https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2 imaging/detection-of-mitoflashes
projective_transformation ip_projective_transformation Projective transformation 2018-12-07 https://github.com/bmcv 0.1.2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 6 33 86 0 0 0 0 0 0 0 0 0 0 0 0 4 14 33 152 https://usegalaxy.eu/published/workflow?id=1eaff95bfeb13890
projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates 2018-12-07 https://github.com/bmcv 0.1.1 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 14 18 20446 21445 0 0 0 0 0 0 0 0 0 0 0 0 14 46 20446 62337 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc
promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them 2019-12-14 https://github.com/phac-nml/promer 1.2 python To update Assembly nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. 2018-04-06 https://github.com/phac-nml/galaxy_tools 1.0.0 perl-bioperl 1.7.8 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
qiime2 qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats 2022-08-26 https://github.com/biocore/deblur 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 37 37 149 149 25 25 54 54 9 9 126 126 3 3 8 8 74 222 337 1011
qiime2 qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac 2022-08-26 https://github.com/qiime2/q2-diversity-lib 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 11 11 23 23 24 24 29 29 22 22 2040 2040 2 2 3 3 59 177 2095 6285
qiime2 qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads 2022-08-26 https://github.com/qiime2/q2-quality-control 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 5 5 5 5 12 12 96 96 3 3 3 3 0 0 0 0 20 60 104 312
qiime2 qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds 2022-08-26 https://github.com/qiime2/q2-phylogeny 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 180 180 512 512 133 133 227 227 62 62 240 240 45 45 89 89 420 1260 1068 3204
qiime2 qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate 2022-08-26 https://github.com/qiime2/q2-metadata 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 196 196 1039 1039 230 230 981 981 45 45 229 229 38 38 263 263 509 1527 2512 7536 https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3
qiime2 qiime2__quality_filter__q_score 2022-08-26 https://github.com/qiime2/q2-quality-filter 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 37 37 11 11 31 31 3 3 59 59 12 12 20 20 44 132 147 441
qiime2 qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp 2022-08-26 https://github.com/qiime2/q2-fragment-insertion 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 18 18 58 58 6 6 43 43 1 1 1 1 2 2 2 2 27 81 104 312 https://usegalaxy.eu/published/workflow?id=6ad6d87618c4e405
qiime2 qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__normalize, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose 2022-08-26 https://github.com/qiime2/q2-feature-table 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 17 17 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 549 549 2231 2231 477 477 1249 1249 181 181 1556 1556 101 101 591 591 1308 3924 5627 16881 https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3
qiime2 qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global 2022-08-26 https://github.com/qiime2/q2-feature-classifier 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 361 361 1476 1476 248 248 715 715 68 68 991 991 61 61 168 168 738 2214 3350 10050 https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4
qiime2 qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask 2022-08-26 https://github.com/qiime2/q2-alignment 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 89 89 336 336 52 52 71 71 16 16 102 102 26 26 67 67 183 549 576 1728
qiime2 qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap 2022-08-26 https://github.com/qiime2/q2-diversity 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 21 21 22 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 484 484 1531 1531 416 416 1321 1321 152 152 687 687 107 107 327 327 1159 3477 3866 11598 https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, https://usegalaxy.org.au/published/workflow?id=543001c51567b438, https://usegalaxy.org/published/workflow?id=c6b6524108f53688, https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318
qiime2 qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__ancombc2, qiime2__composition__ancombc2_visualizer, qiime2__composition__da_barplot, qiime2__composition__tabulate 2022-08-26 https://github.com/qiime2/q2-composition 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 52 52 266 266 48 48 215 215 18 18 255 255 17 17 86 86 135 405 822 2466
qiime2 qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single 2022-08-26 https://github.com/qiime2/q2-cutadapt 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 56 56 240 240 74 74 152 152 12 12 147 147 3 3 31 31 145 435 570 1710
qiime2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single 2022-08-26 http://benjjneb.github.io/dada2/ 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 285 285 1159 1159 264 264 881 881 51 51 320 320 43 43 180 180 643 1929 2540 7620 https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3
qiime2 qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts 2022-08-26 https://github.com/qiime2/q2-demux 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 173 173 708 708 259 259 699 699 50 50 746 746 38 38 126 126 520 1560 2279 6837 https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, https://usegalaxy.eu/published/workflow?id=ca5da5179cefec8b, https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8, https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e, https://usegalaxy.org.au/published/workflow?id=3c1bf73067334071, https://usegalaxy.org.au/published/workflow?id=57aa23f4f0418a07, https://usegalaxy.org.au/published/workflow?id=cddd668a29b1488a, https://usegalaxy.org.au/published/workflow?id=f946d722f7c27479, https://usegalaxy.org/published/workflow?id=0dc387dc861bdb61, https://usegalaxy.org/published/workflow?id=4ca9319c98be08f8, https://usegalaxy.org/published/workflow?id=685b0de4c31f6695, https://usegalaxy.org/published/workflow?id=76b2c4762dd61d03, https://usegalaxy.org/published/workflow?id=7aa87e7f9cfdae78, https://usegalaxy.org/published/workflow?id=a7cc1038b14f2201, https://usegalaxy.org/published/workflow?id=b335f75495dab9b4, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://workflowhub.eu/workflows/893?version=3
qiime2 qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility 2022-08-26 https://github.com/qiime2/q2-longitudinal 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 11 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 19 19 40 40 17 17 47 47 15 15 114 114 4 4 8 8 55 165 209 627
qiime2 qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot 2022-08-26 http://biocore.github.io/emperor/build/html/index.html 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 30 30 86 86 27 27 122 122 13 13 145 145 9 9 27 27 79 237 380 1140
qiime2 qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize 2022-08-26 https://github.com/qiime2/q2-sample-classifier 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 4 4 11 11 20 20 43 43 6 6 6 6 2 2 4 4 32 96 64 192
qiime2 qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table 2022-08-26 https://github.com/qiime2/q2-taxa 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 255 255 1290 1290 158 158 594 594 79 79 408 408 54 54 236 236 546 1638 2528 7584 https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4
qiime2 qiime2__vizard__boxplot, qiime2__vizard__heatmap, qiime2__vizard__lineplot, qiime2__vizard__scatterplot_2d 2024-10-30 https://github.com/qiime2/q2-vizard 0.0.1.dev0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 3 9 3 9
qiime2 qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_bv_brc_genome_features, qiime2__rescript__get_bv_brc_genomes, qiime2__rescript__get_bv_brc_metadata, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_pr2_data, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_reads, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment 2024-04-25 https://github.com/nbokulich/RESCRIPt 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 7 7 0 0 0 0 0 0 0 0 0 0 0 0 4 12 7 21
qiime2 qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref 2022-08-26 https://github.com/qiime2/q2-vsearch 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 66 66 188 188 35 35 169 169 10 10 17 17 48 48 77 77 159 477 451 1353
qiime2 qiime2__stats__alpha_group_significance, qiime2__stats__collate_stats, qiime2__stats__facet_across, qiime2__stats__facet_within, qiime2__stats__mann_whitney_u, qiime2__stats__mann_whitney_u_facet, qiime2__stats__plot_rainclouds, qiime2__stats__prep_alpha_distribution, qiime2__stats__wilcoxon_srt, qiime2__stats__wilcoxon_srt_facet 2024-10-30 https://github.com/qiime2/q2-stats 2025.4.0+q2galaxy.2025.4.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
qiime2 qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq 2022-08-26 https://qiime2.org 2025.4.0+dist.h1147124e To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 2 2 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 546 546 53006 53006 576 576 36664 36664 150 150 4610 4610 64 64 1468 1468 1336 4008 95748 287244 https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, https://usegalaxy.eu/published/workflow?id=ca5da5179cefec8b, https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8, https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e, https://usegalaxy.org.au/published/workflow?id=3c1bf73067334071, https://usegalaxy.org.au/published/workflow?id=543001c51567b438, https://usegalaxy.org.au/published/workflow?id=57aa23f4f0418a07, https://usegalaxy.org.au/published/workflow?id=cddd668a29b1488a, https://usegalaxy.org.au/published/workflow?id=f946d722f7c27479, https://usegalaxy.org/published/workflow?id=0dc387dc861bdb61, https://usegalaxy.org/published/workflow?id=4ca9319c98be08f8, https://usegalaxy.org/published/workflow?id=685b0de4c31f6695, https://usegalaxy.org/published/workflow?id=76b2c4762dd61d03, https://usegalaxy.org/published/workflow?id=7aa87e7f9cfdae78, https://usegalaxy.org/published/workflow?id=a7cc1038b14f2201, https://usegalaxy.org/published/workflow?id=b335f75495dab9b4, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://usegalaxy.org/published/workflow?id=c6b6524108f53688, https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318, https://workflowhub.eu/workflows/893?version=3
quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies 2017-10-05 https://github.com/phac-nml/quasitools 0.7.0 quasitools 0.7.0 Up-to-date Sequence Analysis nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0 12 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 466 466 14252 14252 11 11 27 27 477 1431 14279 42837
rdeval rdeval, rdeval_report rdeval is a General purpose, multithreaded read analysis and manipulation tool. 2025-02-17 https://github.com/vgl-hub/rdeval 0.0.7 rdeval 0.0.7 Up-to-date Assembly richard-burhans https://github.com/vgl-hub/rdeval https://github.com/richard-burhans/galaxytools/tree/main/tools/rdeval 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rdock rdock Docking ligands to proteins and nucleic acids 2016-12-14 https://rdock.github.io/ 1.0 rDock 2013.1 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/rdock 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. 2018-01-31 https://github.com/phac-nml/refseq_masher 0.1.2 refseq_masher 0.1.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 91 91 1546 1546 152 152 611 611 0 0 0 0 19 19 3504 3504 262 786 5661 16983 https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7, https://usegalaxy.eu/published/workflow?id=4216424f032c055f, https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91, https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3, https://usegalaxy.eu/published/workflow?id=b93333efdab316d8, https://usegalaxy.eu/published/workflow?id=fca458178b3c794a, https://usegalaxy.org/published/workflow?id=0e30324072570abb, https://usegalaxy.org/published/workflow?id=4161cfd67ed94b5d, https://usegalaxy.org/published/workflow?id=4d1279007d0137fa, https://usegalaxy.org/published/workflow?id=9ac1e4efe310b3b3, https://usegalaxy.org/published/workflow?id=9e5c5ddb60a24889, https://usegalaxy.org/published/workflow?id=c454c930ccfb0d3f, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://workflowhub.eu/workflows/1043?version=7
repeat_channels repeat_channels Convert single-channel to multi-channel image 2024-04-25 https://github.com/bmcv 1.26.4 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 14 14 0 0 0 0 0 0 0 0 0 0 0 0 5 15 14 42 imaging/voronoi-segmentation
repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. 2023-11-01 https://github.com/repeatexplorer/repex_tarean 2.3.8 To update Genome annotation gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 61 225 225 0 0 0 0 0 0 0 0 0 0 0 0 61 183 225 675
replace_chromosome_names replace_chromosome_names Replace chromosome names 2017-05-18 https://github.com/dpryan79/ChromosomeMappings/ 0.1 python To update Text Manipulation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/replace_chromosome_names 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 59 85 490 579 0 0 0 0 0 0 0 0 0 0 0 0 59 203 490 1559
rfove rfove Perform segmentation region-based fitting of overlapping ellipses 2023-11-12 https://sites.google.com/site/costaspanagiotakis/research/cs 2023.11.12 To update Imaging Image analysis Image analysis Cell biology, Biomedical science, Imaging Cell biology, Biomedical science, Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 15 15 0 0 0 0 0 0 0 0 0 0 0 0 7 21 15 45
scale_image ip_scale_image Scale image 2018-12-07 https://github.com/bmcv 0.18.3 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 14 17 454 521 0 0 0 0 0 0 0 0 0 0 0 0 14 45 454 1429 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc
segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. 2024-04-15 https://github.com/gsneha26/SegAlign 0.1.2.7 segalign-galaxy 0.1.2.7 Up-to-date Next Gen Mappers richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 86 86 379 379 0 0 0 0 0 0 0 0 86 258 379 1137
segmetrics ip_segmetrics Image segmentation and object detection performance measures 2022-10-07 https://github.com/bmcv 1.4 segmetrics 1.5 To update Imaging Image analysis Image analysis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics segmetrics SegMetrics Image segmentation and object detection performance measures segmetrics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 10 10 0 0 0 0 0 0 0 0 0 0 0 0 2 6 10 30 imaging/parameter-tuning
seqtk_nml seqtk_nml_sample Tool to downsample fastq reads 2017-09-19 https://github.com/lh3/seqtk 1.0.1 seqtk 1.5 To update Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sistr_cmd sistr_cmd SISTR in silico serotyping tool 2017-02-20 https://github.com/phac-nml/sistr_cmd 1.1.3 sistr_cmd 1.1.3 Up-to-date Sequence Analysis Genome assembly, Visualisation, Multilocus sequence typing Genome assembly, Visualisation, Multilocus sequence typing Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology nml https://github.com/phac-nml/sistr_cmd https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd SISTR SISTR The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 334 335 4199 4225 0 0 0 0 72 72 638 638 0 0 0 0 406 1219 4837 14537 https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://workflowhub.eu/workflows/407?version=1
skyline2isocor skyline2isocor Converting skyline output to IsoCor input 2024-02-07 https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor 1.0.0 skyline2isocor 1.0.0 Up-to-date Metabolomics workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 115 115 7 21 115 345
slice_image ip_slice_image Slice image 2017-10-30 https://github.com/bmcv 0.3-4 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 5 80 103 0 0 0 0 1 1 24 24 0 0 0 0 5 16 104 335
smalt smalt SMALT aligns DNA sequencing reads with a reference genome. 2017-09-19 http://www.sanger.ac.uk/science/tools/smalt-0 0.7.6 smalt 0.7.6 Up-to-date Sequence Analysis nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
smart_domains smart_domains SMART domains 2017-05-12 https://smart.embl.de/ 0.1.0 perl-bioperl 1.7.8 To update Sequence Analysis earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smart_domains 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
smina smina Scoring and Minimization with smina 2017-07-07 https://sourceforge.net/projects/smina/ 1.0 smina 2017.11.9 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smina 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 17 17 500 500 13 13 49 49 0 0 0 0 0 0 0 0 30 90 549 1647
spades_fasta_header_fixer spades_header_fixer Fixes Spades Fasta ids 2019-12-18 https://github.com/phac-nml/galaxy_tools 1.1.2+galaxy1 sed To update Fasta Manipulation nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. 2023-03-16 https://github.com/HCGB-IGTP/spaTyper 0.3.3 spatyper 0.3.3 Up-to-date Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
split_image ip_split_image Split image along axes 2025-03-07 https://github.com/bmcv 2.2.3 numpy To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 imaging/process-image-bioimageio
split_labelmap ip_split_labelmap Split Labelmaps 2018-12-11 https://github.com/bmcv 0.2-3 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 3 35 51 0 0 0 0 0 0 0 0 0 0 0 0 2 7 35 121
spolpred spolpred A program for predicting the spoligotype from raw sequence reads 2015-12-14 1.0.1 spolpred To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence 2021-07-20 https://github.com/BMCV/galaxy-image-analysis 0.1 giatools 0.4.1 To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 79 79 0 0 0 0 0 0 0 0 0 0 0 0 6 18 79 237 https://dev.workflowhub.eu/workflows/1374?version=1, https://usegalaxy.eu/published/workflow?id=e25f3ca3a1b4e4d8, https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2 imaging/2D-spot-detection, imaging/detection-of-mitoflashes
srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens 2015-12-02 0.3.7 srst2 0.2.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 42 42 316 316 1 1 71 71 0 0 0 0 0 0 0 0 43 129 387 1161 https://workflowhub.eu/workflows/407?version=1
staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. 2018-05-10 https://github.com/phac-nml/staramr 0.11.0 staramr 0.11.0 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr staramr staramr staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2391 2435 25572 26123 1703 1703 11898 11898 952 952 7888 7888 52 52 5414 5414 5098 15338 50772 152867 https://dev.workflowhub.eu/workflows/1107?version=1, https://dev.workflowhub.eu/workflows/1168?version=2, https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=201e65bcf2b71584, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=7, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/470?version=1 genome-annotation/amr-gene-detection, microbiome/plasmid-metagenomics-nanopore
stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) 2016-10-19 1.1.0 stringMLST 0.6.3 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_plasmid_profiler Plasmid Profiler suite defining all dependencies for Plasmid Profiler 2016-11-07 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_qiime2_core 2022-08-29 To update Metagenomics, Statistics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images 2023-06-20 https://github.com/bmcv 0.2.0 superdsm 0.4.0 To update Imaging Image analysis Image analysis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. superdsm 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 26 26 0 0 0 0 0 0 0 0 0 0 0 0 5 15 26 78
t_coffee t_coffee T-Coffee 2016-12-13 https://tcoffee.org/ 13.45.0.4846264 t-coffee 13.46.0.919e8c6b To update Sequence Analysis earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 227 253 3694 9235 1 1 1 1 0 0 0 0 0 0 0 0 228 710 3695 16626 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. 2019-04-15 1.1.0 perl-bioperl 1.7.8 To update Text Manipulation nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
treebest_best treebest_best TreeBeST best 2015-08-06 https://treesoft.sourceforge.net/treebest.shtml 1.9.2.post0 treebest 1.9.2.post1 To update Phylogenetics Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/main/tools/TreeBest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 48 54 994 1025 0 0 0 0 0 0 0 0 0 0 0 0 48 150 994 3013 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal 2017-05-29 https://github.com/galaxy-genome-annotation/python-tripal python-tripal 3.2.1 To update Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
unzip unzip Unzip file 2019-08-01 https://github.com/bmcv 6.0 unzip To update Convert Formats imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1482 1540 7315 7611 1 1 1 1 319 319 2692 2692 39 39 114 114 1841 5581 10122 30662 https://dev.workflowhub.eu/workflows/1254?version=2, https://dev.workflowhub.eu/workflows/1274?version=2, https://dev.workflowhub.eu/workflows/1292?version=2, https://usegalaxy.eu/published/workflow?id=3dbee72d7c550b0c, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=edf7e2128f5aef8d, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://workflowhub.eu/workflows/115?version=1, https://workflowhub.eu/workflows/1208?version=1, https://workflowhub.eu/workflows/655?version=1 ecology/Ecoregionalization_tutorial, ecology/Obitools-metabarcoding, ecology/ecoregiolifetraits, imaging/2D-spot-detection, imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/object-tracking-using-cell-profiler, imaging/voronoi-segmentation, sequence-analysis/Manage_AB1_Sanger, single-cell/scrna-ncbi-anndata
visceral_evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool 2024-09-30 https://github.com/bmcv 0.5-2 visceral-evaluatesegmentation 2015.07.03 To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation evaluatesegmentation-tool 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 1 13 25 0 0 0 0 0 0 0 0 0 0 0 0 1 3 13 51
voronoi_tesselation voronoi_tessellation Compute Voronoi tesselation 2024-03-09 https://github.com/bmcv 0.22.0 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 61 61 0 0 0 0 0 0 0 0 0 0 0 0 4 12 61 183 imaging/voronoi-segmentation
w4mclassfilter w4mclassfilter Filter W4M data by values or metadata 2018-08-06 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper 0.98.19 r-base To update Metabolomics eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9 10 2289 2837 0 0 0 0 4 4 1518 1680 0 0 0 0 13 40 3807 12131
w4mconcatenate W4Mconcatenate [W4M][Utils] concatenate two Metadata tables 2024-07-10 http://workflow4metabolomics.org 1.0.0+galaxy1 r-base To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 4 4 1 3 4 12
w4mcorcov w4mcorcov OPLS-DA Contrasts of Univariate Results 2018-08-06 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper 0.98.18 r-base To update Metabolomics eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11 11 239 376 0 0 0 0 2 2 10 10 0 0 0 0 13 39 249 884
w4mjoinpn w4mjoinpn Join positive- and negative-mode W4M datasets 2018-08-06 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper 0.98.2 coreutils 8.25 To update Metabolomics eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 6 7 149 171 0 0 0 0 2 2 7 7 0 0 0 0 8 25 156 490
wade wade identify regions of interest 2019-09-20 https://github.com/phac-nml/wade 0.2.5+galaxy1 wade 0.2.6 To update Sequence Analysis nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
wsi_extract_top_view ip_wsi_extract_top_view WSI Extract Top View 2017-10-30 https://github.com/bmcv 0.2-2 scikit-image To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 3 25 38 0 0 0 0 0 0 0 0 0 0 0 0 2 7 25 88
xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw 2023-05-24 https://github.com/sneumann/xcms 4.4.0 bioconductor-xcms 4.4.0 Up-to-date Metabolomics Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Biological imaging, Data visualisation, Metabolomics Data visualisation, Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms XCMS xcms Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. 9 11 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 10 9 0 1523 1614 29988 37596 570 570 8230 8230 324 339 5312 5621 8571 8571 2676707 2677268 10988 33070 2720237 8169189 https://dev.workflowhub.eu/workflows/1065?version=1, https://dev.workflowhub.eu/workflows/1119?version=2, https://usegalaxy.eu/published/workflow?id=2179ba1c33f77f7e, https://usegalaxy.fr/published/workflow?id=06fa7dd6eea42350, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://usegalaxy.fr/published/workflow?id=15275ba7c23028ed, https://usegalaxy.fr/published/workflow?id=180744a2f8dca6eb, https://usegalaxy.fr/published/workflow?id=18b2f77f2915adc7, https://usegalaxy.fr/published/workflow?id=192ff9aa79217899, https://usegalaxy.fr/published/workflow?id=19e99a5c09c01bb7, https://usegalaxy.fr/published/workflow?id=26a3e5741d66982a, https://usegalaxy.fr/published/workflow?id=26bdb32c017d798c, https://usegalaxy.fr/published/workflow?id=2ee479308227a926, https://usegalaxy.fr/published/workflow?id=32f903738292a67f, https://usegalaxy.fr/published/workflow?id=3c41c4c5a6332c25, https://usegalaxy.fr/published/workflow?id=49e59327f299e9f7, https://usegalaxy.fr/published/workflow?id=4aa393a1f192a495, https://usegalaxy.fr/published/workflow?id=57748aa2cecf0405, https://usegalaxy.fr/published/workflow?id=5964606a3836cbdf, https://usegalaxy.fr/published/workflow?id=5bfbe77fd6b37c45, https://usegalaxy.fr/published/workflow?id=5ec8a143f82a8c90, https://usegalaxy.fr/published/workflow?id=6895bf9cff915ba1, https://usegalaxy.fr/published/workflow?id=7a790b0acf8ba14d, https://usegalaxy.fr/published/workflow?id=7cc77d6cdd8de027, https://usegalaxy.fr/published/workflow?id=98bb6a831a2b399d, https://usegalaxy.fr/published/workflow?id=b6311795ae10032b, https://usegalaxy.fr/published/workflow?id=bb69fa998b900cb8, https://usegalaxy.fr/published/workflow?id=bcd348178335a19b, https://usegalaxy.fr/published/workflow?id=cca13353d553319e, https://usegalaxy.fr/published/workflow?id=dc17a87057dec748, https://usegalaxy.fr/published/workflow?id=e3d00bdef9addd7c, https://usegalaxy.fr/published/workflow?id=e6a55d00f1364794, https://usegalaxy.fr/published/workflow?id=e6f26a543c3e044a, https://usegalaxy.fr/published/workflow?id=f49e102f63d3e2bb, https://usegalaxy.org.au/published/workflow?id=f9e5caaf08a450ec, https://usegalaxy.org.au/published/workflow?id=fa0243ff9b5ca997, https://usegalaxy.org/published/workflow?id=3edd2957ecd26d6c, https://usegalaxy.org/published/workflow?id=aeeaf3e06a13bc22, https://workflowhub.eu/workflows/677?version=1, https://workflowhub.eu/workflows/680?version=1 metabolomics/gc_ms_with_xcms, metabolomics/gcms, metabolomics/lcms, metabolomics/lcms-preprocessing
10x_bamtofastq 10x_bamtofastq Converts 10x Genomics BAM to FASTQ 2022-05-10 https://github.com/10XGenomics/bamtofastq 1.4.1 10x_bamtofastq 1.4.1 Up-to-date Convert Formats, Single Cell bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 321 321 11 11 21 21 2 2 25 25 0 0 0 0 102 306 367 1101
Wound healing scratch assay image analysis woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays 2024-02-29 https://git.embl.de/grp-cba/wound-healing-htm-screen 1.6.1 fiji-morpholibj 1.6.1 Up-to-date Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 31 31 0 0 0 0 0 0 0 0 0 0 0 0 1 3 31 93 https://workflowhub.eu/workflows/782?version=1
add_line_to_file add_line_to_file Adds a text line to the beginning or end of a file. 2020-11-01 0.1.0 coreutils 8.25 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 410 410 17866 17866 257 257 1873 1873 39 39 496 496 0 0 0 0 706 2118 20235 60705 https://dev.workflowhub.eu/workflows/1257?version=1, https://usegalaxy.eu/published/workflow?id=1b10ece62e745125, https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=5cbaaf2fe80b52a2, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://usegalaxy.eu/published/workflow?id=d1357759d0962144, https://usegalaxy.eu/published/workflow?id=dd73bdcbac8649a3, https://usegalaxy.eu/published/workflow?id=e3b0b521ee8f2aef, https://usegalaxy.eu/published/workflow?id=ff2fd4a4bb27d859, https://usegalaxy.org.au/published/workflow?id=5cd804644a34c8fd, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, https://usegalaxy.org/published/workflow?id=195a608c481040de, https://usegalaxy.org/published/workflow?id=28c7e8269d478244, https://usegalaxy.org/published/workflow?id=634bbef1f67a0e30, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/249?version=2, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1, https://workflowhub.eu/workflows/794?version=2 microbiome/pathogen-detection-from-nanopore-foodborne-data, single-cell/bulk-music-2-preparescref
add_value addValue Add a value as a new column. 2012-12-04 1.0.1 perl To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 1 0 1 1 1 1 1 1 1378 1747 48863 386572 1230 6294 19044 297704 210 244 4193 4765 29 30 238 248 2847 14009 72338 833965 https://dev.workflowhub.eu/workflows/1014?version=1, https://dev.workflowhub.eu/workflows/1113?version=2, https://dev.workflowhub.eu/workflows/1199?version=2, https://dev.workflowhub.eu/workflows/1204?version=2, https://dev.workflowhub.eu/workflows/1246?version=2, https://dev.workflowhub.eu/workflows/1250?version=2, https://dev.workflowhub.eu/workflows/1324?version=3, https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.eu/published/workflow?id=1031e4c4f18e020e, https://usegalaxy.eu/published/workflow?id=171d6fca2c3339e2, 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agat agat GTF/GFF analysis toolkit 2023-05-22 https://github.com/NBISweden/AGAT 1.4.0 agat 1.4.2 To update Convert Formats, Statistics, Fasta Manipulation Data handling, Genome annotation Data handling, Genome annotation Genomics Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 339 339 5444 5444 57 57 302 302 28 28 485 485 7 7 140 140 431 1293 6371 19113 https://usegalaxy.org/published/workflow?id=951575e9a352301c, https://workflowhub.eu/workflows/1096?version=2
align_back_trans align_back_trans Thread nucleotides onto a protein alignment (back-translation) 2014-02-18 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 To update Fasta Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 36 556 588 0 0 0 0 0 0 0 0 0 0 0 0 33 102 556 1700
antarna antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . 2015-04-30 1.1 antarna 2.0.1.2 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 7 284 306 0 0 0 0 0 0 0 0 0 0 0 0 5 17 284 874
antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters 2015-02-28 https://antismash.secondarymetabolites.org 6.1.1 antismash 8.0.1 To update Sequence Analysis Sequence clustering, Gene prediction, Differential gene expression analysis Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Molecular interactions, pathways and networks, Gene and protein families bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 852 962 24780 25468 795 795 7459 7459 210 210 7834 7834 0 0 0 0 1857 5681 40073 120907 https://dev.workflowhub.eu/workflows/1145?version=1, https://usegalaxy.eu/published/workflow?id=0461bbd1f96292e2, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=edbaf66c1e97ebdb, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 genome-annotation/secondary-metabolite-discovery
aresite2 AREsite2_REST AREsite2 REST Interface 2017-02-01 http://rna.tbi.univie.ac.at/AREsite 0.1.2 python To update RNA, Data Source, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11 13 52 76 0 0 0 0 0 0 0 0 0 0 0 0 11 35 52 180 https://usegalaxy.eu/published/workflow?id=4e57c5cf750afadd
atactk_trim_adapters atactk_trim_adapters Trim adapters from paired-end HTS reads. 2018-06-20 https://github.com/ParkerLab/atactk/ 0.1.6 atactk 0.1.9 To update Fastq Manipulation rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 65 78 223 291 0 0 0 0 0 0 0 0 0 0 0 0 65 208 223 737
bamhash bamhash Hash BAM and FASTQ files to verify data integrity 2015-09-17 https://github.com/DecodeGenetics/BamHash 1.1 bamhash 1.1 Up-to-date Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 50 134 188 0 0 0 0 0 0 0 0 0 0 0 0 45 140 134 456
barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm 2016-06-11 https://github.com/YeoLab/gscripts 0.1.0 pysam 0.23.2 To update RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
basecoverage gops_basecoverage_1 Base Coverage of all intervals 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 18 35 192 308 287 2291 1957 45635 23 36 363 545 1 2 3 13 329 3022 2515 51531 https://usegalaxy.org/published/workflow?id=6f836f4b71d399e7, https://usegalaxy.org/published/workflow?id=baf01109a1bf8d0d, https://usegalaxy.org/published/workflow?id=e3c1736cca484dda
best_regression_subsets BestSubsetsRegression1 Perform Best-subsets Regression 2014-04-01 1.0.0 numpy To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 5 3 5 9 74 16 255 0 0 0 0 0 0 0 0 12 103 19 298
bg_statistical_hypothesis_testing bg_statistical_hypothesis_testing Tool for computing statistical tests. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy To update Statistics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 65 183 364 1 1 1 1 0 0 0 0 0 0 0 0 48 162 184 733
bia_download bia_download Tool to query ftp links for study from bioimage archive 2023-12-06 https://www.ebi.ac.uk/biostudies/bioimages/studies 0.2.0 wget To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 13 13 0 0 0 0 0 0 0 0 0 0 0 0 7 21 13 39
bigwig_to_bedgraph bigwig_to_bedgraph Convert from bigWig to bedGraph format 2015-06-04 0.1.0 ucsc_tools To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 641 753 6696 7952 0 0 0 0 0 1 0 3 0 0 0 0 641 2036 6696 21347
bioimage_inference bioimage_inference Load model from BioImage.IO and make inferences 2024-08-02 https://github.com/bgruening/galaxytools 2.4.1 python To update Imaging Machine learning, Computer science Machine learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging pytorch PyTorch PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. pytorch 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 4 4 59 59 0 0 0 0 0 0 0 0 0 0 0 0 4 12 59 177 imaging/process-image-bioimageio
biomodels biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. 2023-11-07 https://www.ebi.ac.uk/biomodels/ 1.1 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 112 112 1 1 1 1 0 0 0 0 0 0 0 0 20 60 113 339
bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data 2021-05-17 https://bionanogenomics.com/ 3.7.0 To update Assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 156 156 556 556 52 52 157 157 22 22 722 722 0 0 0 0 230 690 1435 4305 https://dev.workflowhub.eu/workflows/1002?version=1, https://dev.workflowhub.eu/workflows/1187?version=2, https://usegalaxy.eu/published/workflow?id=075c4126e66def01, https://usegalaxy.eu/published/workflow?id=2e6ed783bdf05d16, https://usegalaxy.eu/published/workflow?id=319bc351f7a8e358, https://usegalaxy.eu/published/workflow?id=3d047ed984762ce8, https://usegalaxy.eu/published/workflow?id=45c0933b5c522628, https://usegalaxy.eu/published/workflow?id=5bb7691b176d1010, https://usegalaxy.eu/published/workflow?id=bb13f30a5562d30d, https://usegalaxy.eu/published/workflow?id=f6bd10486a0ba17d, https://usegalaxy.org.au/published/workflow?id=02f2a556e77eed14, https://usegalaxy.org.au/published/workflow?id=11f1564f2bd815d8, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=53cbacc71790c41b, https://usegalaxy.org.au/published/workflow?id=73565f6cb4136370, https://usegalaxy.org.au/published/workflow?id=87bbf9408b3f2a32, https://usegalaxy.org.au/published/workflow?id=bcb0be4f4a0e369f, https://usegalaxy.org/published/workflow?id=85f521f5c7351406, https://usegalaxy.org/published/workflow?id=b1cfa3c239ef2523, https://usegalaxy.org/published/workflow?id=bff8bc8d0059274f, https://usegalaxy.org/published/workflow?id=ca3f2d9554e9e1c8, https://usegalaxy.org/published/workflow?id=d5183b025d0e78dd, https://workflowhub.eu/workflows/643?version=5 assembly/vgp_genome_assembly
bismark bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states 2015-02-28 https://www.bioinformatics.babraham.ac.uk/projects/bismark/ 0.22.1 bismark 0.24.2 To update Sequence Analysis, Next Gen Mappers bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1030 1202 14830 16831 0 0 0 0 37 37 729 729 17 17 66 66 1084 3424 15625 48876 https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2
black_forest_labs_flux black_forest_labs_flux Using the black forest labs FLUX.1 models to generate image based on user input. 2024-10-14 https://github.com/bgruening/galaxytools/tree/master/tools/flux 2024 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flux https://github.com/bgruening/galaxytools/tree/master/tools/flux 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 99 99 0 0 0 0 0 0 0 0 0 0 0 0 31 93 99 297
blat_coverage_report generate_coverage_report Polymorphism of the Reads 2014-05-19 1.0.0 To update Next Gen Mappers, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blat_mapping blat2wig Coverage of the Reads in wiggle format 2014-05-19 1.0.0 To update Next Gen Mappers, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. 2022-11-04 https://blobtoolkit.genomehubs.org/ 4.0.7 To update Sequence Analysis, Assembly Genome assembly, Scaffolding, Visualisation, Data deposition, Data parsing Genome assembly, Scaffolding, Visualisation Sequence assembly, Model organisms, Workflows, Phylogenomics, Zoology, Biodiversity Sequence assembly, Model organisms, Workflows, Phylogenomics, Zoology, Biodiversity bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit BlobToolKit BlobToolKit BlobToolKit Viewer is a genome-scale dataset visualistion tool developed as part of the blobtoolkit project to allow browser-based identification and filtering of target and non-target data in genome assemblies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 107 107 2014 2014 18 18 69 69 38 38 580 580 0 0 0 0 163 489 2663 7989 https://dev.workflowhub.eu/workflows/1127?version=3, https://usegalaxy.eu/published/workflow?id=3069c17b52decab4, https://usegalaxy.eu/published/workflow?id=88f80a31e3ff8663, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=c9a8fba4c56f5c83, https://usegalaxy.org.au/published/workflow?id=0a3fb089674de144, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 assembly/ERGA-post-assembly-QC
blockbuster blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. 2015-02-28 http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html 0.1.2 blockbuster 0.0.1.1 To update RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 98 123 744 3051 14 14 19 19 9 9 314 314 0 0 0 0 121 388 1077 5538 https://dev.workflowhub.eu/workflows/1333?version=1, https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=4f40ae432d8a4259, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=667d05ae290d11ea, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=b36be9100485e6cd, https://usegalaxy.eu/published/workflow?id=c7026cd5578c8678, https://usegalaxy.eu/published/workflow?id=f00b862b06093636, https://usegalaxy.org.au/published/workflow?id=4a7f22081ecde089 transcriptomics/small_ncrna_clustering
blockclust blockclust BlockClust detects transcripts with similar processing patterns. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust 1.1.1 blockclust 1.1.1 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 53 83 793 1572 34 34 79 79 15 15 637 637 0 0 0 0 102 336 1509 5306 https://dev.workflowhub.eu/workflows/1333?version=1, https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=667d05ae290d11ea, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=c7026cd5578c8678, https://usegalaxy.eu/published/workflow?id=f00b862b06093636, https://usegalaxy.org.au/published/workflow?id=4a7f22081ecde089 transcriptomics/small_ncrna_clustering
bowtie_wrappers bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. 2012-11-26 http://bowtie-bio.sourceforge.net/ 1.2.0 bowtie 1.3.1 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 1338 1569 25579 26908 531 17497 10209 203807 328 388 17416 17754 0 2 0 82 2197 23850 53204 354959 https://dev.workflowhub.eu/workflows/1149?version=2, https://usegalaxy.org.au/published/workflow?id=5cf5334877cc1297, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org/published/workflow?id=07739fbbd53755f6, https://usegalaxy.org/published/workflow?id=0b3af7e9ac69a6b7, https://usegalaxy.org/published/workflow?id=11dac9cba49be089, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=1b385fd45ee48614, https://usegalaxy.org/published/workflow?id=246da6fd63cbd49d, https://usegalaxy.org/published/workflow?id=29a80db9f3208c29, https://usegalaxy.org/published/workflow?id=31dea5361ec9421c, https://usegalaxy.org/published/workflow?id=344a79d4f12d2cff, https://usegalaxy.org/published/workflow?id=3d1f4bd67ce30f99, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=486ee20613d58dcf, https://usegalaxy.org/published/workflow?id=48adcc44fe62a99c, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=4aad96570d252f95, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=58d16d45527990b7, https://usegalaxy.org/published/workflow?id=5aa2caa2dcae1477, https://usegalaxy.org/published/workflow?id=62401f33a369bac0, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=85c3a1fc1d3d3df8, https://usegalaxy.org/published/workflow?id=92a233e5f2405830, https://usegalaxy.org/published/workflow?id=a24092b7f00b4e2a, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=ab23c641cfdefe0c, https://usegalaxy.org/published/workflow?id=b0a12221ce09c001, https://usegalaxy.org/published/workflow?id=b2176abeb937f026, https://usegalaxy.org/published/workflow?id=b5c79535c499bc58, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://usegalaxy.org/published/workflow?id=d2864aa3631b3bf6, https://usegalaxy.org/published/workflow?id=d2b798962b35dad9, https://usegalaxy.org/published/workflow?id=dcb73fce390b36b2, https://usegalaxy.org/published/workflow?id=eb20150175a6ab03, https://usegalaxy.org/published/workflow?id=f201ce61becf9a80, https://usegalaxy.org/published/workflow?id=f823b87dd06ba4ac, https://usegalaxy.org/published/workflow?id=fc09d17e0bce18f8, https://usegalaxy.org/published/workflow?id=fe3d4001499c3f15 genome-annotation/tnseq
canonical_correlation_analysis cca1 Canonical Correlation Analysis 2014-05-19 1.0.0 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 17 19 58 77 26 147 113 505 0 0 0 0 0 0 0 0 43 252 171 924
canu canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). 2018-06-07 https://github.com/marbl/canu 2.2 canu 2.3 To update De-novo assembly De-novo assembly Genomics Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1517 1626 13461 15728 0 0 0 0 414 424 3666 3839 29 29 337 337 1960 5999 17464 54832
categorize_elements_satisfying_criteria categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. 2013-09-25 1.0.0 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4 5 28 41 0 0 0 0 13 15 172 208 0 0 0 0 17 54 200 649
ccat peakcalling_ccat Control-based ChIP-seq Analysis Tool 2014-01-27 0.0.2 ccat 3.0 To update ChIP-seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 27 42 76 179 0 0 0 0 0 0 0 0 0 0 0 0 27 96 76 331
cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads 2015-04-28 0.0.1 cd-hit-auxtools 4.8.1 To update Metagenomics, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 456 691 6201 7789 0 0 0 0 0 0 0 0 456 1603 6201 20191 https://usegalaxy.org/published/workflow?id=35c2626849348f2c
cellpose cellpose Cellpose is an anatomical segmentation algorithm 2024-02-29 https://github.com/MouseLand/cellpose 3.1.0 To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 22 22 0 0 0 0 0 0 0 0 0 0 0 0 5 15 22 66
cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper 2020-03-06 To update Imaging Quantification, Image analysis, Parsing Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype Imaging, Microarray experiment, Genotype and phenotype bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler CellProfiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. cellprofiler 0 23 23 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 23 19 0 773 773 4932 4932 0 0 0 0 108 108 6930 6930 0 0 0 0 881 2643 11862 35586 https://dev.workflowhub.eu/workflows/1254?version=2, https://dev.workflowhub.eu/workflows/1262?version=2, https://usegalaxy.eu/published/workflow?id=3dbee72d7c550b0c, https://usegalaxy.eu/published/workflow?id=4a41ea1eb6752171, https://workflowhub.eu/workflows/115?version=1, https://workflowhub.eu/workflows/41?version=2 imaging/object-tracking-using-cell-profiler, imaging/tutorial-CP
cellprofiler4 cp_cellprofiler4 cellProfiler4 wrapper 2021-09-15 https://github.com/CellProfiler/CellProfiler 4.2.8 To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 55 55 0 0 0 0 0 0 0 0 0 0 0 0 11 33 55 165
change_case ChangeCase Convert column case. 2012-12-04 1.0.1 perl To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 1 0 1 1 1 1 1 1 2386 2846 11597 13931 1975 2661 9987 18262 255 262 982 1001 90 91 632 652 4706 15272 23198 80242 https://dev.workflowhub.eu/workflows/1326?version=3, https://dev.workflowhub.eu/workflows/1345?version=1, https://dev.workflowhub.eu/workflows/606?version=1, https://dev.workflowhub.eu/workflows/759?version=1, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.org.au/published/workflow?id=2cef9a1633e0a067, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=e75a7802d2941f31 transcriptomics/ref-based
chatgpt_openai_api chatgpt_openai_api Using the OpenAI GPT models to generate text based on user input. 2024-08-12 https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 2024 python To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 35 546 546 0 0 0 0 0 0 0 0 0 0 0 0 35 105 546 1638
chipseeker chipseeker A tool for ChIP peak annotation and visualization 2018-05-24 https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html 1.32.0 bioconductor-chipseeker 1.42.0 To update ChIP-seq, Genome annotation rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 1049 1136 19348 22173 2630 2954 34564 37281 111 114 3489 3571 0 0 0 0 3790 11784 57401 177827 https://usegalaxy.eu/published/workflow?id=6bce1d419a179c50, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.org/published/workflow?id=7643e66a9b4e9c11
chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython 2013-09-26 0.0.3 biopython 1.70 To update Graphics, Sequence Analysis, Visualization peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
circexplorer circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) 2016-06-06 https://github.com/YangLab/CIRCexplorer 1.1.9.0 circexplorer 1.1.10 To update Sequence Analysis, RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 31 42 162 279 0 0 0 0 6 6 247 247 0 0 0 0 37 122 409 1344 https://usegalaxy.org.au/published/workflow?id=5aff01d0b5fabd84
clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio 2013-10-28 https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.22 To update Assembly, Next Gen Mappers, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cleanlab cleanlab_issue_handler CleanLab is a package to find various types of issues in a dataset. 2025-05-05 https://cleanlab.ai 2.7.1 cleanlab To update Machine Learning bgruening https://github.com/cleanlab/cleanlab https://github.com/bgruening/galaxytools/tree/master/tools/cleanlab 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins 2013-05-02 http://www.compbio.dundee.ac.uk/www-nod/ 0.1.0 clinod 1.3 To update Sequence Analysis Nucleic acid sequence analysis Nucleic acid sequence analysis Sequence analysis Sequence analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 23 559 559 0 0 0 0 0 0 0 0 23 69 559 1677
cluster gops_cluster_1 Cluster the intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 16 37 497 864 145 1552 1957 30668 17 20 1358 1449 1 2 1 11 179 1969 3813 40618 https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.org/published/workflow?id=6f836f4b71d399e7, https://usegalaxy.org/published/workflow?id=7cff5c4dadffaad5
cmsearch_deoverlap cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. 2023-08-19 https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl 0.08+galaxy2 perl To update RNA Comparison, Alignment Comparison, Alignment Biology, Medicine Biology, Medicine rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results.This tool removes lower-scoring overlaps from cmsearch results. Given information about the clans and the cmsearch tbl output this tool returns a filtered cmsearch tbl output. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 2982 2982 0 0 0 0 0 0 0 0 0 0 0 0 3 9 2982 8946 https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://workflowhub.eu/workflows/1270?version=1
cmv cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. 2017-09-22 https://github.com/eggzilla/cmv 1.0.8 cmv 1.0.8 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 11 15 70 114 0 0 0 0 0 0 0 0 0 0 0 0 11 37 70 254 https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1
cofold cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. 2015-02-28 http://www.e-rna.org/cofold/ 2.0.4.0 cofold 2.0.4 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25 31 257 361 0 0 0 0 0 0 0 0 0 0 0 0 25 81 257 875
column_arrange_by_header bg_column_arrange_by_header Column arrange by header name 2015-03-02 0.2 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 452 506 7117 7491 444 444 2235 2235 111 142 1582 1820 27 27 193 193 1034 3187 11127 33993 https://dev.workflowhub.eu/workflows/1081?version=1, https://usegalaxy.eu/published/workflow?id=0f7acf235096b708, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=33f23578677b384d, https://usegalaxy.eu/published/workflow?id=4f62794453f65cba, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=83049910e2cd5128, https://usegalaxy.eu/published/workflow?id=8f677efac7100097, https://usegalaxy.eu/published/workflow?id=930a9757252d3ca6, https://usegalaxy.eu/published/workflow?id=9a0275211e74698a, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://usegalaxy.eu/published/workflow?id=ff2fd4a4bb27d859, https://usegalaxy.org.au/published/workflow?id=20d472fc5563a640, https://usegalaxy.org.au/published/workflow?id=4f837b7f90d5ebac, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1 single-cell/bulk-deconvolution-evaluate, variant-analysis/somatic-variants
combine_metaphlan2_humann2 combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances 2023-07-20 0.3.0 python To update Metagenomics Aggregation Aggregation Metagenomics, Molecular interactions, pathways and networks Metagenomics, Molecular interactions, pathways and networks bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 80 80 614 614 18 18 29 29 0 0 0 0 0 0 0 0 98 294 643 1929 https://usegalaxy.eu/published/workflow?id=9472be79da012999
compalignp compalignp Compute fractional identity between trusted alignment and test alignment 2015-06-03 1.0 compalignp 1.0 Up-to-date RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 29 29 222 0 0 0 0 0 0 0 0 0 0 0 0 5 39 29 280
compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information 2022-10-19 0.2.0 To update Metagenomics Comparison Comparison Metagenomics, Gene and protein families Metagenomics, Gene and protein families bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 27 32 285 332 0 0 0 0 0 0 0 0 0 0 0 0 27 86 285 902
complement gops_complement_1 Complement intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 11 20 133 233 160 838 438 4818 8 8 381 485 0 0 0 0 179 1224 952 7440
compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. 2013-09-25 1.0.0 To update Sequence Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10 12 70 98 0 0 0 0 8 8 328 376 0 0 0 0 18 56 398 1270
compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. 2013-09-25 1.0.0 To update Sequence Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 2 40 65 0 0 0 0 5 5 327 377 0 0 0 0 6 19 367 1176
compute_q_values compute_q_values Compute q-values based on multiple simultaneous tests p-values 2014-04-01 1.0.1 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 35 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 35
concat gops_concat_1 Concatenate two bed files 2014-04-01 https://github.com/galaxyproject/gops 1.0.1 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 688 815 576916 577315 652 3572 43601 85947 106 120 19341 19463 28 29 1224 1234 1474 7484 641082 1966123 https://dev.workflowhub.eu/workflows/194?version=2, https://usegalaxy.eu/published/workflow?id=06544e74f583fd05, https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977, https://usegalaxy.eu/published/workflow?id=3aaea772745ca295, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=522500fac247be6f, https://usegalaxy.eu/published/workflow?id=5ded4002e684a02c, https://usegalaxy.eu/published/workflow?id=6c91fe92ef069d64, https://usegalaxy.eu/published/workflow?id=7b7d6a5c6c65d74b, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.eu/published/workflow?id=b8fc492025ad6ff0, https://usegalaxy.eu/published/workflow?id=c832ecfa83bcda14, https://usegalaxy.fr/published/workflow?id=0df61a88d64de252, https://usegalaxy.fr/published/workflow?id=a3e9062133fdf7c2, https://usegalaxy.fr/published/workflow?id=bf8ffe72b7ce4570, https://usegalaxy.org.au/published/workflow?id=2955ea7be1cdda29, https://usegalaxy.org.au/published/workflow?id=2b71eb1dc2aa28a1, https://usegalaxy.org.au/published/workflow?id=4b681937a01df465, https://usegalaxy.org.au/published/workflow?id=5cd7f1824db7a960, https://usegalaxy.org.au/published/workflow?id=6795e545b0cafded, https://usegalaxy.org.au/published/workflow?id=851552cc3e830253, https://usegalaxy.org.au/published/workflow?id=a77ce877e786d44a, https://usegalaxy.org.au/published/workflow?id=daff6854b5dfc6f1, https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886, https://usegalaxy.org.au/published/workflow?id=ebd1ee73906fdea0, https://usegalaxy.org.au/published/workflow?id=f65b54fcffaa11e5, https://usegalaxy.org/published/workflow?id=0392de36b6f55a8f, https://usegalaxy.org/published/workflow?id=27e1a8c651d9a298, https://usegalaxy.org/published/workflow?id=31cc891be77cbc6f, https://usegalaxy.org/published/workflow?id=4ffdb2cf21759d26, https://usegalaxy.org/published/workflow?id=507c817755b2410d, https://usegalaxy.org/published/workflow?id=65f3a5772ae05a7a, https://usegalaxy.org/published/workflow?id=6ba03802169c0063, https://usegalaxy.org/published/workflow?id=7b20a62d69d53efc, https://usegalaxy.org/published/workflow?id=d136d24e4c96962a, https://usegalaxy.org/published/workflow?id=f25a3da4b00eddbb, https://workflowhub.eu/workflows/1270?version=1, https://workflowhub.eu/workflows/138?version=5, https://workflowhub.eu/workflows/356?version=1
condense_characters Condense characters1 Condense consecutive characters. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 371 39 2177 8 9 199 226 0 1 0 10 32 445 238 2889
convert_characters Convert characters1 Convert delimiters to tab. 2012-12-04 1.0.1 python To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 1 0 1 1 1 1 1 1 1117 1307 28630 34674 2285 8875 21394 162126 256 344 5315 6614 131 132 1374 1462 3789 18236 56713 318302 https://dev.workflowhub.eu/workflows/1002?version=1, https://dev.workflowhub.eu/workflows/1187?version=2, https://dev.workflowhub.eu/workflows/1250?version=2, https://usegalaxy.eu/published/workflow?id=002a51bdef00e14d, https://usegalaxy.eu/published/workflow?id=023a0ee62dd1f593, https://usegalaxy.eu/published/workflow?id=03be9d62e8e4a129, https://usegalaxy.eu/published/workflow?id=085c3a4c89d137b5, https://usegalaxy.eu/published/workflow?id=089e5e83b1de0511, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, 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convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides 2014-05-19 1.0.0 To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs 2017-11-01 https://github.com/PatrickRWright/CopraRNA 2.1.1 coprarna 2.1.4 To update RNA, Sequence Analysis rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
correlation cor2 Correlation for numeric columns 2014-07-28 1.0.0 rpy To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 110 143 395 896 93 756 327 5569 21 28 199 263 8 8 19 19 232 1399 940 8627
count_gff_features count_gff_features Count GFF Features 2014-07-28 0.2 galaxy-ops 1.1.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 123 139 283 332 335 653 773 1411 55 81 488 589 10 10 19 19 523 1929 1563 5477 https://dev.workflowhub.eu/workflows/1380?version=1 microbiome/metaplasmidome_query
count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file 2016-02-05 https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.22 To update Assembly, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
coverage gops_coverage_1 Coverage of a set of intervals on second set of intervals 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 43 60 1663 1858 183 2116 3611 44240 14 18 291 369 1 2 4 14 241 2678 5569 57619 https://usegalaxy.eu/published/workflow?id=668a9f5da768fa30, https://usegalaxy.eu/published/workflow?id=99c4dce722c023d1, https://usegalaxy.org/published/workflow?id=08ca80ae36c8c576, https://usegalaxy.org/published/workflow?id=468c5a8fe7a40778, https://usegalaxy.org/published/workflow?id=9cc814d43379c2a6, https://usegalaxy.org/published/workflow?id=e6550f5289099efc
coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth 2014-11-20 https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.22 To update Assembly, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cpat cpat Coding-potential assessment tool using an alignment-free logistic regression model. 2023-02-01 https://github.com/liguowang/cpat 3.0.5 cpat 3.0.5 Up-to-date Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 56 56 228 228 70 70 298 298 11 11 173 173 0 0 0 0 137 411 699 2097 https://dev.workflowhub.eu/workflows/1324?version=3, https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://usegalaxy.org.au/published/workflow?id=a1b97364f84022cf, https://workflowhub.eu/workflows/878?version=1 transcriptomics/differential-isoform-expression
create_tool_recommendation_model create_tool_recommendation_model Create model to recommend tools 2019-08-20 https://github.com/bgruening/galaxytools 0.0.5 python To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 26 331 448 33 33 74 74 0 0 0 0 0 0 0 0 59 177 405 1332
crispr_recognition_tool crispr_recognition_tool CRISPR Recognition Tool 2015-02-28 1.2.0 crisper_recognition_tool 1.2 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 200 218 4369 4491 0 0 0 0 0 0 0 0 0 0 0 0 200 618 4369 13229
ctd_batch ctdBatch_1 CTD analysis of chemicals, diseases, or genes 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 39 50 182 219 1 161 1 447 0 0 0 0 0 0 0 0 40 291 183 1032 https://usegalaxy.org/published/workflow?id=44b27a1296633366
cummerbund cummeRbund Wrapper for the Bioconductor cummeRbund library 2015-04-24 https://bioconductor.org/packages/release/bioc/html/cummeRbund.html 2.16.0 fonts-conda-ecosystem To update RNA, Visualization devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 88 168 1077 1812 451 2050 2948 15186 55 159 2429 3574 0 0 0 0 594 3565 6454 33480 https://usegalaxy.eu/published/workflow?id=17e720bee3b9104f, https://usegalaxy.org.au/published/workflow?id=189c584ea4bde59a, https://usegalaxy.org.au/published/workflow?id=1ac197bae296b2bf, https://usegalaxy.org.au/published/workflow?id=427e27f87b8048a3, https://usegalaxy.org.au/published/workflow?id=581c455f74aa55a4, https://usegalaxy.org.au/published/workflow?id=80a1493fb9593bb3, https://usegalaxy.org.au/published/workflow?id=cc6de673126c56cb, https://usegalaxy.org.au/published/workflow?id=d3989c6c2c663cd3, https://usegalaxy.org/published/workflow?id=82681bd5f059e39a
cummerbund_to_tabular cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. 2014-12-22 1.0.1 To update Convert Formats, Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 31 97 641 1208 91 484 877 2691 0 0 0 0 0 0 0 0 122 825 1518 6935 https://usegalaxy.eu/published/workflow?id=17e720bee3b9104f, https://usegalaxy.org/published/workflow?id=82681bd5f059e39a
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https://usegalaxy.org/published/workflow?id=ff3ade25b35f4893, https://usegalaxy.org/published/workflow?id=fff1a5c7475b3eeb, https://workflowhub.eu/workflows/1054?version=1, https://workflowhub.eu/workflows/1057?version=3, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1063?version=3, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/109?version=9, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1201?version=3, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/248?version=4, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/561?version=11, https://workflowhub.eu/workflows/603?version=2, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/612?version=15, https://workflowhub.eu/workflows/622?version=11, https://workflowhub.eu/workflows/624?version=1, https://workflowhub.eu/workflows/625?version=13, https://workflowhub.eu/workflows/629?version=1, https://workflowhub.eu/workflows/633?version=15, https://workflowhub.eu/workflows/641?version=16, https://workflowhub.eu/workflows/642?version=14, https://workflowhub.eu/workflows/643?version=5, https://workflowhub.eu/workflows/645?version=8, https://workflowhub.eu/workflows/655?version=1, https://workflowhub.eu/workflows/689?version=1, https://workflowhub.eu/workflows/698?version=1, https://workflowhub.eu/workflows/751?version=9, https://workflowhub.eu/workflows/794?version=2, https://workflowhub.eu/workflows/876?version=1, https://workflowhub.eu/workflows/880?version=1 assembly/assembly-decontamination, assembly/ecoli_comparison, contributing/create-new-tutorial, data-science/data-manipulation-olympics, digital-humanities/text_mining_chinese, ecology/Obitools-metabarcoding, ecology/ref-based-rad-seq, epigenetics/atac-seq, epigenetics/ewas-suite, galaxy-interface/workflow-reports, genome-annotation/bacterial-comparative-genomics-dataset-construction, genome-annotation/gene-centric, genome-annotation/tnseq, introduction/data-manipulation-olympics, introduction/galaxy-intro-101-everyone, introduction/galaxy-intro-peaks2genes, introduction/galaxy-reproduce, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/clinical-mp-4-quantitation, microbiome/metaplasmidome_query, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/clinical-mp-4-quantitation, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq, proteomics/metaquantome-data-creation, proteomics/neoantigen-7-hla-binding-novel-peptides, sequence-analysis/tapscan-streptophyte-algae, single-cell/GO-enrichment, single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music-2-preparescref, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_alevin, single-cell/scrna-case_alevin-combine-datasets, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-data-ingest, single-cell/scrna-ncbi-anndata, single-cell/scrna-seurat-pbmc3k, statistics/gpu_jupyter_lab, transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/mirna-target-finder, transcriptomics/network-analysis-with-heinz, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways, transcriptomics/rna-seq-viz-with-heatmap2, variant-analysis/non-dip, variant-analysis/pox-tiled-amplicon, visualisation/circos, visualisation/circos-microbial
delete_overlapping_indels delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6 7 26 40 0 0 0 0 0 0 0 0 0 0 0 0 6 19 26 92
dewseq dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data 2022-10-20 https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers 0.1.0+galaxy0 python To update Sequence Analysis, RNA, CLIP-seq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 96 96 0 0 0 0 0 0 0 0 0 0 0 0 20 60 96 288
dgidb_annotator dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) 2013-11-28 0.1 To update Systems Biology, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 30 52 69 0 133 0 304 0 0 0 0 0 0 0 0 26 215 52 477
diff diff GNU diff tool that calculates the differences between two files. 2020-03-29 http://www.gnu.org/software/diffutils/ 3.10 diffutils To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 105 105 397 397 26 26 44 44 0 0 0 0 0 0 0 0 131 393 441 1323 digital-humanities/text_mining_chinese
diffbind Diffbind provides functions for processing ChIP-Seq data. 2015-02-28 http://bioconductor.org/packages/release/bioc/html/DiffBind.html To update ChIP-seq bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind https://github.com/bgruening/galaxytools/tree/master/tools/diffbind 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
divide_pg_snp dividePgSnp Separate pgSnp alleles into columns 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 10 25 38 21 55 67 174 0 0 0 0 0 0 0 0 30 125 92 396
dorina dorina_search data source for RNA interactions in post-transcriptional regulation 2015-05-20 1.0 To update RNA, Data Source rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 31 767 1639 0 0 0 0 0 0 0 0 0 0 0 0 4 39 767 3173
dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) 2015-06-10 5.7.a rnastructure 6.4 To update Sequence Analysis, RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dotknot dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence 2015-09-17 http://dotknot.csse.uwa.edu.au/ 1.3.1 vienna_rna To update RNA, Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 15 60 88 0 0 0 0 0 0 0 0 0 0 0 0 12 39 60 208
draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria 2013-09-25 1.0.0 R To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 51 57 187 224 0 0 0 0 21 33 185 236 7 7 9 9 79 255 381 1231
dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences 2014-01-27 1.0.1 r-waveslim 1.7.5 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 11 157 162 0 0 0 0 8 27 157 476
dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features 2014-01-27 1.0.1 r-waveslim 1.7.5 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 145 145 0 0 0 0 7 21 145 435
dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences 2014-01-27 1.0.1 r-waveslim 1.7.5 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 7 142 144 0 0 0 0 5 17 142 428
dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences 2014-01-27 1.0.1 r-waveslim 1.7.5 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 8 152 153 0 0 0 0 7 22 152 457
dwt_var_perfeature dwt_var1 Wavelet variance using Discrete Wavelet Transfoms 2014-01-27 1.0.2 r-bitops To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2 4 23 36 4 4 11 11 5 7 210 241 2 2 2 2 13 43 246 782
edta edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 2022-10-16 https://github.com/oushujun/EDTA edta 2.2.2 To update Variant Analysis De-novo assembly, Deisotoping, Genome annotation De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta https://github.com/bgruening/galaxytools/tree/master/tools/edta edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 129 129 4601 4601 0 0 0 0 0 0 0 0 0 0 0 0 129 387 4601 13803
effectivet3 effectiveT3 Find bacterial type III effectors in protein sequences 2013-04-30 http://effectors.org 0.0.21 effectiveT3 1.0.1 To update Sequence Analysis Sequence classification Sequence classification Sequence analysis Sequence analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
epicseg epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. 2018-03-02 https://github.com/lamortenera/epicseg @VERSION_STRING@ epicseg 1.0 To update Epigenetics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg https://github.com/bgruening/galaxytools/tree/master/tools/epicseg 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 22 135 255 0 0 0 0 0 0 0 0 0 0 0 0 18 58 135 525
erga_ear make_ear A tool to compile assembly reports and stastics from assembly pipeline 2024-06-07 https://github.com/ERGA-consortium/EARs/tree/main 24.10.15 reportlab To update Sequence Analysis, Assembly bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 83 83 0 0 0 0 0 0 0 0 0 0 0 0 3 9 83 249
exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. 2015-02-28 http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp 1.0.1 exparna 1.0.1 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
express express Quantify the abundances of a set of target sequences from sampled subsequences 2014-01-27 1.1.1 eXpress 1.5.1 To update RNA devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 46 258 338 0 117 0 1184 22 60 2426 2903 0 0 0 0 54 331 2684 9793
fasta_compute_length fasta_compute_length Compute sequence length 2014-05-19 https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length 1.0.4 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 1106 1318 9829 10754 1432 5802 18807 52942 177 211 5259 5507 14 15 320 330 2729 12804 34215 137963 https://dev.workflowhub.eu/workflows/1078?version=1, https://dev.workflowhub.eu/workflows/1113?version=2, https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=2f053b615d9788bf, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=6e1fe7372e93fae0, https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://usegalaxy.eu/published/workflow?id=a31100610fba17a1, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=b77e3b08092fa73e, https://usegalaxy.eu/published/workflow?id=c696b37d1bf68e9b, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.eu/published/workflow?id=e522be58f0bac656, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.org.au/published/workflow?id=5cfea39918e8632d, https://usegalaxy.org.au/published/workflow?id=6b1b0a945d367b4c, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=386d3b300cf05305, https://usegalaxy.org/published/workflow?id=400c1d170f073279, https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=89d3c800d3be6050, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=c88fe3dc11bc4905, https://usegalaxy.org/published/workflow?id=cfa9e6e722b086c8, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c, https://workflowhub.eu/workflows/439?version=2, https://workflowhub.eu/workflows/880?version=1 assembly/ecoli_comparison, sequence-analysis/viral_primer_design, single-cell/scatac-batch-correction-snapatac2, single-cell/scatac-standard-processing-snapatac2, variant-analysis/pox-tiled-amplicon
fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species 2014-05-19 0.0.1 bx-python 0.13.0 To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 254 288 41122 41245 608 1453 14273 19773 97 119 2169 2271 5 6 270 280 964 3794 57834 179237 https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe
fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) 2017-02-02 https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fasta_filter_by_length fasta_filter_by_length Filter sequences by length 2014-05-19 1.2 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 956 1100 51262 62177 1464 3864 49515 103992 263 309 4018 5788 23 24 336 346 2706 10709 105131 382565 https://dev.workflowhub.eu/workflows/1113?version=2, https://dev.workflowhub.eu/workflows/1132?version=2, https://dev.workflowhub.eu/workflows/1197?version=2, https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.org.au/published/workflow?id=9c60b83feaa22415, https://usegalaxy.org.au/published/workflow?id=b59fada651043735, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org.au/published/workflow?id=fc3c83b11f527977, https://usegalaxy.org/published/workflow?id=1708fdfd1d485434, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5 assembly/assembly-with-preprocessing, assembly/ecoli_comparison
fasta_to_tabular fasta2tab FASTA-to-Tabular converter 2014-05-19 1.1.1 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 1713 1998 117694 125685 2161 8740 68214 195704 282 354 5750 7961 35 37 884 903 4191 19511 192542 715337 https://dev.workflowhub.eu/workflows/1026?version=1, https://dev.workflowhub.eu/workflows/1042?version=1, https://dev.workflowhub.eu/workflows/1077?version=2, https://dev.workflowhub.eu/workflows/1091?version=1, https://dev.workflowhub.eu/workflows/1199?version=2, https://dev.workflowhub.eu/workflows/1201?version=2, https://dev.workflowhub.eu/workflows/1204?version=2, https://dev.workflowhub.eu/workflows/1240?version=1, https://dev.workflowhub.eu/workflows/1354?version=1, https://dev.workflowhub.eu/workflows/1369?version=1, https://dev.workflowhub.eu/workflows/1386?version=1, https://dev.workflowhub.eu/workflows/1398?version=1, https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=0ed8817a90caa2b1, https://usegalaxy.eu/published/workflow?id=1031e4c4f18e020e, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=5e1b048040ea7535, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, 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fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) 2017-02-02 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_info fastq_info FASTQ info allows to validate single or paired fastq files 2021-09-12 https://github.com/nunofonseca/fastq_utils 0.25.1 fastq_utils 0.25.2 To update Fastq Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1502 1502 15141 15141 1952 1952 8408 8408 0 0 0 0 0 0 0 0 3454 10362 23549 70647 https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a
fastq_pair_names fastq_pair_names Extract FASTQ paired read names 2014-05-05 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.2.0 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.2.0 To update Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_trimmer_by_quality fastq_quality_trimmer FASTQ Quality Trimmer by sliding window 2014-01-27 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 984 1146 5468 7027 3351 11668 28522 100961 259 360 2229 2900 104 104 281 281 4698 22674 36500 184169 https://usegalaxy.eu/published/workflow?id=b6eb5fe7e37f680a, https://usegalaxy.org.au/published/workflow?id=0fc7c14c4d1ac8f5, https://usegalaxy.org.au/published/workflow?id=427e27f87b8048a3, https://usegalaxy.org.au/published/workflow?id=9176f8ebac92d10c, https://usegalaxy.org.au/published/workflow?id=d3989c6c2c663cd3, https://usegalaxy.org/published/workflow?id=1cd08f3549cf5589, https://usegalaxy.org/published/workflow?id=1d1ee1fad4e20eeb, https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3fbaa9ae67362495, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=61d324b1eca6300e, https://usegalaxy.org/published/workflow?id=712d9ae42b45c4b9, https://usegalaxy.org/published/workflow?id=7253824f78a90431, https://usegalaxy.org/published/workflow?id=73d98e5f821a78b3, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=98c2e50add031fce, https://usegalaxy.org/published/workflow?id=c64719e91e7346a2, https://usegalaxy.org/published/workflow?id=cd14df23bb05db2c, https://usegalaxy.org/published/workflow?id=d69ea491b99016f4, https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f, https://usegalaxy.org/published/workflow?id=e2fa6584853a0dee, https://usegalaxy.org/published/workflow?id=ea69f4fbdbb88c71
fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data 2014-05-19 1.0.0 To update Convert Formats, Fastq Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 8 0 0 0 0 0 0 0 0 0 3 0 8
featurecounter featureCoverage1 Feature coverage 2014-04-01 2.0.0 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 16 20 22289 22389 53 349 311 13711 0 0 0 0 0 0 0 0 69 507 22600 81300 https://usegalaxy.org/published/workflow?id=4b52f6a8dcfc8045, https://usegalaxy.org/published/workflow?id=66748e20a243eafe
ffmpeg ffmpeg_converter A complete, cross-platform solution to record, convert and stream audio and video. 2025-04-21 https://ffmpeg.org 0.1.0 ffmpeg To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/ffmpeg https://github.com/bgruening/galaxytools/tree/master/tools/ffmpeg 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_transcripts_via_tracking filter_combined_via_tracking Filter Combined Transcripts 2014-01-27 0.1 To update RNA devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8 10 21 24 20 242 51 638 2 2 2 2 0 0 0 0 30 314 74 812
find_diag_hits find_diag_hits Find diagnostic hits 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.1 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 12 51 70 1 204 3 1787 0 0 0 0 0 0 0 0 10 236 54 1965
find_subsequences bg_find_subsequences 2015-03-19 0.3 biopython 1.70 To update bgruening https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 63 80 518 817 271 383 2854 3449 3 3 134 134 0 0 0 0 337 1140 3506 11412 https://dev.workflowhub.eu/workflows/1149?version=2, https://usegalaxy.eu/published/workflow?id=b86f3775aa1f13bc genome-annotation/tnseq
flanking_features flanking_features_1 Fetch closest non-overlapping feature for every interval 2014-04-01 https://github.com/galaxyproject/gops 4.0.1 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 50 64 542 761 279 2565 2173 32930 16 23 1256 1448 2 3 14 24 347 3349 3985 43133 https://usegalaxy.org/published/workflow?id=6471aa8abbb3fa40, https://usegalaxy.org/published/workflow?id=7bc71a005c6f18d0
flexynesis flexynesis, flexynesis_cbioportal_import This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. 2024-08-12 https://github.com/BIMSBbioinfo/flexynesis/tree/main 0.2.18 flexynesis 0.2.19 To update Machine Learning, Statistics, Systems Biology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 13 13 0 0 0 0 0 0 0 0 0 0 0 0 2 6 13 39
flye flye Assembly of long and error-prone reads. 2018-09-22 https://github.com/fenderglass/Flye/ 2.9.6 flye 2.9.6 Up-to-date Assembly Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Sequence assembly, Metagenomics, Whole genome sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3861 3923 38698 39063 3259 3259 24739 24739 1844 1848 11434 11596 165 165 902 902 9129 27453 75773 227846 https://dev.workflowhub.eu/workflows/1005?version=1, https://dev.workflowhub.eu/workflows/1006?version=1, https://dev.workflowhub.eu/workflows/1091?version=1, https://dev.workflowhub.eu/workflows/1131?version=2, https://dev.workflowhub.eu/workflows/1139?version=1, https://dev.workflowhub.eu/workflows/1170?version=2, https://dev.workflowhub.eu/workflows/1178?version=1, https://usegalaxy.eu/published/workflow?id=0ebfab0e957b7267, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=201e65bcf2b71584, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=30b514cfb9cce524, https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=77e5bbd317750915, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=9ddb703e1db13504, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=b2dfa74f55a73409, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=cf8591391a17a914, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.org.au/published/workflow?id=02c74095a7128c9d, https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060, https://usegalaxy.org.au/published/workflow?id=1ad4c47cee851dda, https://usegalaxy.org.au/published/workflow?id=22bd45f60c60a338, https://usegalaxy.org.au/published/workflow?id=2cb16d321a804b1a, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=479c6b0a96ea1610, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=5b32e2f0d390a4ba, https://usegalaxy.org.au/published/workflow?id=7c343e5b55474d19, https://usegalaxy.org.au/published/workflow?id=803ef29108e36e58, https://usegalaxy.org.au/published/workflow?id=b5403e4fff2961f9, https://usegalaxy.org.au/published/workflow?id=c4d23297f6fbf5f3, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=d832905fbaf2ca31, https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2, https://usegalaxy.org/published/workflow?id=0602c14704dbe1ff, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=5626a440a5798458, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=bff206b4625375bc, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://usegalaxy.org/published/workflow?id=c8d74054c1820087, https://usegalaxy.org/published/workflow?id=cce88bc57b180d09, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/1114?version=1, https://workflowhub.eu/workflows/225?version=1, https://workflowhub.eu/workflows/51?version=1, https://workflowhub.eu/workflows/750?version=2, https://workflowhub.eu/workflows/788?version=1 assembly/chloroplast-assembly, assembly/hifi-assembly, assembly/largegenome, assembly/mrsa-nanopore, microbiome/pathogen-detection-from-nanopore-foodborne-data
footprint footprint Find transcription factor footprints 2017-04-18 https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ 1.0.0 footprint 1.0.1 To update Epigenetics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint https://github.com/bgruening/galaxytools/tree/master/tools/footprint 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 5 57 57 0 0 0 0 0 0 0 0 0 0 0 0 5 15 57 171
format_cd_hit_output format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file 2022-10-19 1.0.0+galaxy1 To update Fasta Manipulation bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 62 66 219 244 0 0 0 0 0 0 0 0 0 0 0 0 62 190 219 682
format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels 2022-10-19 0.2.0 To update Metagenomics Formatting Formatting Taxonomy, Metagenomics Taxonomy, Metagenomics bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 590 661 6183 6878 0 0 0 0 0 0 0 0 0 0 0 0 590 1841 6183 19244 https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b
generate_pc_lda_matrix generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA 2014-07-28 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 32 120 140 104 270 482 1057 14 17 190 220 2 2 2 2 150 621 794 3007
get_flanks get_flanks1 Get flanks returns flanking region/s for every gene 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1571 2250 3815 325334 2179 6691 8758 242476 114 149 794 1126 8 9 11 21 3872 16843 13378 595713 https://dev.workflowhub.eu/workflows/1102?version=1, https://dev.workflowhub.eu/workflows/120?version=1, https://usegalaxy.eu/published/workflow?id=d2ef6d4a2189c0a6, https://usegalaxy.eu/published/workflow?id=f30c8054f064ac9f, https://usegalaxy.org.au/published/workflow?id=19e3488987d58d73, https://usegalaxy.org/published/workflow?id=013bf76cb3a8bd66, https://usegalaxy.org/published/workflow?id=4f02edb5c9bb84ab, https://usegalaxy.org/published/workflow?id=888bfce1c214ab64, https://usegalaxy.org/published/workflow?id=8a3e457a9453c313, https://usegalaxy.org/published/workflow?id=94de815260acc3a8, https://usegalaxy.org/published/workflow?id=c2b299627d2baf48, https://usegalaxy.org/published/workflow?id=f25a3da4b00eddbb introduction/galaxy-intro-peaks2genes
get_orfs_or_cdss get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 185 185 1009 1009 0 0 0 0 250 250 1605 1605 7 9 63 70 442 1328 2677 8038 https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a, https://usegalaxy.eu/published/workflow?id=a1518a029132ee3d, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6, https://usegalaxy.org.au/published/workflow?id=0f71c97671bb401f, https://usegalaxy.org.au/published/workflow?id=cb6f49d4ebfa0891
getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments 2014-04-01 1.0.0 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 87 48 291 0 0 0 0 0 0 0 0 18 123 48 387
getindels_2way getIndels_2way Fetch Indels from pairwise alignments 2014-04-01 1.0.0 numpy To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 61 55 237 0 0 0 0 0 0 0 0 24 109 55 347
gfastats gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. 2022-03-08 https://github.com/vgl-hub/gfastats 1.3.11 gfastats 1.3.11 Up-to-date Sequence Analysis Data handling Data handling Computational biology Computational biology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 865 865 13937 13937 501 501 9026 9026 128 128 3152 3152 0 0 0 0 1494 4482 26115 78345 https://dev.workflowhub.eu/workflows/1127?version=3, https://dev.workflowhub.eu/workflows/1359?version=1, https://usegalaxy.eu/published/workflow?id=002a51bdef00e14d, 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gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.1.1 taxonomy 0.10.1 To update Metagenomics Database search, ID mapping Database search, ID mapping Taxonomy Taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 74 110 483 683 18 1798 122 14058 0 0 0 0 1 1 2 6 93 2095 607 15961 https://usegalaxy.org/published/workflow?id=02c9244e2fb060de, https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c, https://usegalaxy.org/published/workflow?id=fe3d4001499c3f15
glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) 2015-02-28 https://ccb.jhu.edu/software/glimmerhmm/ To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gmaj gmaj_1 GMAJ Multiple Alignment Viewer 2014-01-27 2.0.1 To update Visualization devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 7 12 12 25 230 78 984 7 8 10 11 1 1 1 1 40 326 101 1210
gotohscan rbc_gotohscan Find subsequences in db 2015-07-02 1.3.0 gotohscan 1.3 To update Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 7 26 72 0 0 0 0 0 0 0 0 0 0 0 0 5 17 26 124
graph_converter graph_converter Convert between different graph formats 2015-02-28 0.1.0 To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
graphclust graphclust GraphClust can be used for structural clustering of RNA sequences. 2015-02-28 http://www.bioinf.uni-freiburg.de/Software/GraphClust/ 0.1 GraphClust To update RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 6
graphclust_aggregate_alignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. 2018-10-24 0.6.0 graphclust-wrappers 0.6.0 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 14 17 38 120 0 0 0 0 0 0 0 0 0 0 0 0 14 45 38 196
graphclust_align_cluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. 2018-10-22 0.1 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 23 25 164 3101 0 0 0 0 0 0 0 0 0 0 0 0 23 71 164 3429
graphclust_cmfinder cmFinder Determines consensus motives for sequences. 2016-12-15 0.4 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 41 58 23273 50693 0 0 0 0 0 0 0 0 0 0 0 0 41 140 23273 97239 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphclust_fasta_to_gspan gspan Second step of GraphClust 2016-12-15 0.4 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 26 82 161 0 0 0 0 0 0 0 0 0 0 0 0 20 66 82 325
graphclust_mlocarna locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. 2016-12-15 0.4 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 41 58 23307 50825 0 0 0 0 0 0 0 0 0 0 0 0 41 140 23307 97439 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphclust_motif_finder_plot motifFinderPlot Plotting results for GraphClust 2017-02-22 0.4 seaborn To update RNA rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 8 10 36 71 0 0 0 0 0 0 0 0 0 0 0 0 8 26 36 143
graphclust_nspdk NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. 2016-12-15 9.2.3.1 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 91 128 2586 62905 0 0 0 0 0 0 0 0 0 0 0 0 91 310 2586 68077 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphclust_postprocessing glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. 2016-12-15 0.5 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 46 63 881 2131 0 0 0 0 0 0 0 0 0 0 0 0 46 155 881 3893 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphclust_postprocessing_no_align graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. 2018-10-25 0.5 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 3 27 108 0 0 0 0 0 0 0 0 0 0 0 0 1 5 27 162
graphclust_prepocessing_for_mlocarna preMloc This tool prepares files for locarna step. 2016-12-15 0.4 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 46 64 962 2140 0 0 0 0 0 0 0 0 0 0 0 0 46 156 962 4064 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphclust_preprocessing preproc Preprocessing input for GraphClust 2016-12-15 0.5 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 53 73 952 1921 0 0 0 0 0 0 0 0 0 0 0 0 53 179 952 3825 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick 2016-12-26 http://www.graphicsmagick.org 1.3.45 graphicsmagick 1.3.26 To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 96 106 1640 2803 3 3 3 3 0 0 0 0 0 0 0 0 99 307 1643 6092 https://dev.workflowhub.eu/workflows/1195?version=2, https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=0b2304aa2083bd1a, https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=4f0f3b911b4e4921, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc, https://usegalaxy.eu/published/workflow?id=6afc245029ce5008, https://usegalaxy.eu/published/workflow?id=b4bfcbf8acee9cc3, https://workflowhub.eu/workflows/807?version=1 climate/pangeo, ecology/x-array-map-plot, galaxy-interface/workflow-posters
graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. 2018-09-27 https://github.com/isovic/graphmap/ 0.5.2 graphmap 0.6.4 To update Assembly Sequence trimming, EST assembly, Read mapping Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing Gene transcripts, RNA-Seq, RNA splicing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 336 370 6719 7528 0 0 0 0 0 0 0 0 0 0 0 0 336 1042 6719 20966
graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. 2018-05-24 https://github.com/dmaticzka/GraphProt 1.1.7+galaxy2 graphprot 1.1.7 To update Sequence Analysis, RNA, CLIP-seq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 21 425 496 0 0 0 0 0 0 0 0 0 0 0 0 20 61 425 1346 https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf
hclust2 hclust2 Plots heatmaps 2018-07-22 https://bitbucket.org/nsegata/hclust2/ 0.99 hclust2 1.0.0 To update Data Visualization rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hgv_fundo hgv_funDo FunDO human genes associated with disease terms 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 27 397 104 1794 0 0 0 0 0 0 0 0 27 451 104 2002
hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve 2013-09-25 https://www.ebi.ac.uk/huber-srv/hilbert/ 1.0.0 R To update Graphics, Visualization devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 14 60 117 265 0 0 0 0 0 0 0 0 14 88 117 499
hictk hictk Convert cooler to juicebox_hic 2024-02-03 https://github.com/paulsengroup/hictk 2.0.2 hictk 2.1.2 To update Convert Formats, Epigenetics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk https://github.com/bgruening/galaxytools/tree/master/tools/hictk 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 51 51 0 0 0 0 0 0 0 0 0 0 0 0 14 42 51 153
hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. 2017-03-09 https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html 0.9.2 To update Epigenetics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup https://github.com/bgruening/galaxytools/tree/master/tools/hicup 7 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 6 0 181 211 851 1095 146 146 691 691 0 0 0 0 0 0 0 0 327 1011 1542 4870 https://usegalaxy.eu/published/workflow?id=57b96a59cca0e8df, https://usegalaxy.eu/published/workflow?id=7d49f41cd294e15b, https://usegalaxy.eu/published/workflow?id=83fea2e4508bc3ed, https://usegalaxy.eu/published/workflow?id=cbe9e09ed3e91e2e, https://usegalaxy.org/published/workflow?id=2ffae50d0916b641, https://usegalaxy.org/published/workflow?id=43cea919ebf9d978, https://usegalaxy.org/published/workflow?id=748c1a9d85eb61e2, https://usegalaxy.org/published/workflow?id=ba4815ec62edab04
hisat hisat HISAT is a fast and sensitive spliced alignment program. 2015-05-13 http://ccb.jhu.edu/software/hisat/index.shtml 1.0.3 hisat To update Assembly devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 228 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 228
histogram histogram_rpy Histogram of a numeric column 2014-07-28 https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram 1.0.5 rpy2 2.7.8 To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 894 1088 3757 4808 1558 7347 6227 49220 138 267 503 794 170 172 449 557 2760 14394 10936 77251 https://dev.workflowhub.eu/workflows/1037?version=1, https://dev.workflowhub.eu/workflows/1140?version=2, https://dev.workflowhub.eu/workflows/1163?version=2, https://dev.workflowhub.eu/workflows/1167?version=2, https://dev.workflowhub.eu/workflows/1215?version=2, https://dev.workflowhub.eu/workflows/1380?version=1, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=a2b386eef5645acd, https://usegalaxy.org.au/published/workflow?id=43a951ec514498f6, https://usegalaxy.org.au/published/workflow?id=781457327e644c7e, https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc, https://usegalaxy.org/published/workflow?id=07739fbbd53755f6, https://usegalaxy.org/published/workflow?id=13a550ed56b56502, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=25adc55d2a26e34b, https://usegalaxy.org/published/workflow?id=9cc814d43379c2a6, https://usegalaxy.org/published/workflow?id=d2864aa3631b3bf6, https://usegalaxy.org/published/workflow?id=f823b87dd06ba4ac microbiome/metaplasmidome_query, proteomics/DIA_Analysis_MSstats, proteomics/maxquant-label-free, proteomics/protein-quant-sil
homer Software for motif discovery and next generation sequencing analysis. 2015-02-28 http://homer.salk.edu/homer/ To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
htseq_clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets 2022-10-11 https://github.com/EMBL-Hentze-group/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 To update Sequence Analysis, RNA, CLIP-seq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 106 106 0 0 0 0 0 0 0 0 0 0 0 0 21 63 106 318
illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. 2015-05-05 http://fiji.sc 20240614 To update Imaging Image analysis, Image annotation, Visualisation Image analysis, Image annotation, Visualisation Imaging Imaging imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 imagej ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. imagej2 0 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 0 118 120 1337 1768 0 0 0 0 0 0 0 0 0 0 0 0 118 356 1337 4442 https://workflowhub.eu/workflows/1259?version=1
indels_3way indels_3way Fetch Indels from 3-way alignments 2013-09-25 1.0.3 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 11 22 3 21 25 292 0 0 0 0 0 0 0 0 4 30 36 386
infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. 2015-02-28 http://infernal.janelia.org/ 1.1.5 infernal 1.1.5 Up-to-date RNA Nucleic acid feature detection Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics Sequence sites, features and motifs, Structural genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal infernal Infernal Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 240 316 55882 114704 3 3 4 4 34 35 1207 1361 0 0 0 0 277 908 57093 230255 https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977, https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1, https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7, https://workflowhub.eu/workflows/1270?version=1
inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. 2015-02-28 http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
instagraal instagraal Large genome reassembly based on Hi-C data 2022-11-10 https://github.com/koszullab/instaGRAAL 0.1.6 To update Assembly Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 15 15 159 159 0 0 0 0 0 0 0 0 0 0 0 0 15 45 159 477
intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. 2017-02-09 https://github.com/BackofenLab/IntaRNA 3.4.1 intarna 3.4.1 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 41 48 3116 7713 0 0 0 0 0 0 0 0 0 0 0 0 41 130 3116 13945
intersect gops_intersect_1 Intersect the intervals of two datasets 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 2402 3168 20481 350925 4538 14563 46292 782991 471 580 6122 7689 71 73 539 559 7482 33348 73434 1289032 https://dev.workflowhub.eu/workflows/1102?version=1, https://dev.workflowhub.eu/workflows/1110?version=1, https://dev.workflowhub.eu/workflows/1111?version=1, https://dev.workflowhub.eu/workflows/1173?version=2, https://usegalaxy.eu/published/workflow?id=013cc98f55b01d5d, https://usegalaxy.eu/published/workflow?id=0edf0e9a778cb732, https://usegalaxy.eu/published/workflow?id=24ef0d03f58d4fc5, https://usegalaxy.eu/published/workflow?id=4516fe237a7112cc, https://usegalaxy.eu/published/workflow?id=68f7300f922f548d, https://usegalaxy.eu/published/workflow?id=69eed719f9b5b99d, https://usegalaxy.eu/published/workflow?id=6a48604ef9ceb8b8, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=941bc727b61c09ab, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=ad636a8e1763580a, https://usegalaxy.eu/published/workflow?id=c4cefff5b812aae9, https://usegalaxy.eu/published/workflow?id=d2ef6d4a2189c0a6, https://usegalaxy.eu/published/workflow?id=f30c8054f064ac9f, https://usegalaxy.org.au/published/workflow?id=19e3488987d58d73, https://usegalaxy.org.au/published/workflow?id=a9e52a40b63d26fc, https://usegalaxy.org.au/published/workflow?id=b0b8b8f79b467cf6, https://usegalaxy.org.au/published/workflow?id=f27f6ed478d7a258, https://usegalaxy.org/published/workflow?id=013bf76cb3a8bd66, https://usegalaxy.org/published/workflow?id=27e1a8c651d9a298, https://usegalaxy.org/published/workflow?id=30507545aa971637, https://usegalaxy.org/published/workflow?id=37383240151a472a, https://usegalaxy.org/published/workflow?id=4375f00f8a285088, https://usegalaxy.org/published/workflow?id=44b27a1296633366, https://usegalaxy.org/published/workflow?id=4f02edb5c9bb84ab, https://usegalaxy.org/published/workflow?id=56530f4d41413832, https://usegalaxy.org/published/workflow?id=58d16d45527990b7, https://usegalaxy.org/published/workflow?id=60b080dc16141121, https://usegalaxy.org/published/workflow?id=7942748c29d718f8, https://usegalaxy.org/published/workflow?id=888bfce1c214ab64, https://usegalaxy.org/published/workflow?id=8e5efd04399c6838, https://usegalaxy.org/published/workflow?id=8e9882d890ee5ec7, https://usegalaxy.org/published/workflow?id=9005ecd577bd9bfa, https://usegalaxy.org/published/workflow?id=9238f7208033d0d6, https://usegalaxy.org/published/workflow?id=b1cd3f793187d667, https://usegalaxy.org/published/workflow?id=baf01109a1bf8d0d, https://usegalaxy.org/published/workflow?id=c2b299627d2baf48, https://usegalaxy.org/published/workflow?id=e3c1736cca484dda, https://usegalaxy.org/published/workflow?id=e4f6b68301aafd38, https://usegalaxy.org/published/workflow?id=ebac500f62f4a469, https://usegalaxy.org/published/workflow?id=f365c53b5024d7f1, https://usegalaxy.org/published/workflow?id=f637ea9a753cfbe8 genome-annotation/gene-centric, introduction/galaxy-intro-peaks2genes, introduction/galaxy-intro-strands
iprscan5 Interproscan queries the interpro database and provides annotations. 2015-02-28 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
itsx itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. 2022-05-02 https://microbiology.se/software/itsx/ 1.1.3 itsx 1.1.3 Up-to-date Metagenomics Sequence feature detection Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Functional, regulatory and non-coding RNA, Microbiology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 95 95 2207 2207 0 0 0 0 5 5 28 28 0 0 0 0 100 300 2235 6705
jbrowse2 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool 2024-06-04 https://jbrowse.org 2.17.0 jbrowse2 3.5.1 To update Sequence Analysis Genome visualisation, Structure visualisation, Pathway visualisation Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Mapping, Structural variation, Genomics, Gene structure, Sequence assembly fubar https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 360 360 2065 2065 156 156 551 551 48 48 308 308 0 0 0 0 564 1692 2924 8772 https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2cd5670f075704ab, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=84414f3441946702, https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=386d3b300cf05305, https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf, https://usegalaxy.org/published/workflow?id=89d3c800d3be6050 epigenetics/formation_of_super-structures_on_xi
join gops_join_1 Join the intervals of two datasets side-by-side 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 1565 2481 14974 331127 8818 39713 47410 515332 188 292 1253 1701 32 33 170 180 10603 63725 63807 975954 https://usegalaxy.eu/published/workflow?id=04b838103aed1929, https://usegalaxy.eu/published/workflow?id=29346872085adf1f, https://usegalaxy.eu/published/workflow?id=2f7149d02db43b7b, https://usegalaxy.eu/published/workflow?id=3e91f8417a66d02c, https://usegalaxy.eu/published/workflow?id=4a33a8348ac03f00, https://usegalaxy.eu/published/workflow?id=51cce3b98da3e822, https://usegalaxy.eu/published/workflow?id=579a56c129883cf3, 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join_files_on_column_fuzzy join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. 2017-11-26 1.0.1 python To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 311 419 1814 2719 0 0 0 0 45 45 1204 1204 6 6 16 16 362 1194 3034 10007 https://dev.workflowhub.eu/workflows/1123?version=1, https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73, https://usegalaxy.eu/published/workflow?id=e573c6b697524e3a, https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89 metabolomics/msi-finding-nglycans
kernel_canonical_correlation_analysis kcca1 Kernel Canonical Correlation Analysis 2014-05-19 1.0.0 rpy To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4 4 46 70 33 78 186 352 0 0 0 0 0 0 0 0 37 156 232 886
kernel_principal_component_analysis kpca1 Kernel Principal Component Analysis 2014-05-19 1.0.0 rpy To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 25 32 111 159 82 251 249 717 0 0 0 0 4 4 7 7 111 509 367 1617
kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. 2015-02-28 http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. 2015-08-05 https://bitbucket.org/natefoo/taxonomy 1.2+galaxy0 gawk To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1179 1182 24986 24999 1734 2302 16477 25867 472 472 17180 17180 0 0 0 0 3385 10726 58643 185332 https://usegalaxy.eu/published/workflow?id=0bafeb17c21ebc9c, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=bd4e3cdc7f29049b, https://usegalaxy.eu/published/workflow?id=ca80039c4933aa0a, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://usegalaxy.eu/published/workflow?id=ee0005a5487653ba, https://usegalaxy.org/published/workflow?id=a63927dd19759714, https://usegalaxy.org/published/workflow?id=b68ec42db8953569, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/101?version=1, https://workflowhub.eu/workflows/124?version=1
labels bg_labels remaps and annotates alignments 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lastz_paired_reads lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads 2012-11-26 1.1.1 lastz 1.04.52 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2 4 2 9 0 0 0 0 5 5 8 10 0 0 0 0 7 23 10 39
lca_wrapper lca1 Find lowest diagnostic rank 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.1 taxonomy 0.10.1 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4 20 68 137 14 1112 112 6136 0 0 0 0 0 0 0 0 18 1168 180 6633 https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c
lda_analysis lda_analy1 Perform Linear Discriminant Analysis 2014-07-28 1.0.1 R To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 47 51 140 164 99 323 777 1570 0 3 0 4 4 4 17 17 150 681 934 3623
lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data 2016-06-04 https://github.com/mourisl/Lighter 1.0 lighter 1.1.3 To update Sequence Analysis, Fasta Manipulation k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics Whole genome sequencing, DNA, Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 29 32 144 180 0 0 0 0 0 0 0 0 0 0 0 0 29 90 144 468
linear_regression LinearRegression1 Perform Linear Regression 2014-04-01 1.0.1 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 279 141 1131 0 0 0 0 0 0 0 0 33 345 141 1413 https://usegalaxy.org/published/workflow?id=857db984ff571191
locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs 2015-02-28 http://www.bioinf.uni-freiburg.de/Software/LocARNA/ 2.0.1 locarna 2.0.1 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 47 317 358 0 0 0 0 0 0 0 0 0 0 0 0 36 119 317 992 https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73
logistic_regression_vif LogisticRegression Perform Logistic Regression with vif 2014-04-01 1.0.1 numpy To update Sequence Analysis, Variant Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 48 45 173 0 0 0 0 0 0 0 0 12 72 45 263
maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file 2014-04-01 1.0.0 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 28 47 356 0 0 0 0 0 0 0 0 6 40 47 450
mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences 2015-06-16 https://mafft.cbrc.jp/alignment/software/ 7.526 mafft 7.525 To update RNA Multiple sequence alignment Multiple sequence alignment Sequence analysis Sequence analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 2 0 0 0 0 0 2 2 2 0 2260 2371 188287 190662 4700 6141 114726 130987 1134 1265 21429 22090 156 156 1783 1783 8250 26433 326225 997972 https://dev.workflowhub.eu/workflows/1173?version=2, https://dev.workflowhub.eu/workflows/1296?version=2, https://dev.workflowhub.eu/workflows/40?version=1, https://dev.workflowhub.eu/workflows/42?version=1, https://dev.workflowhub.eu/workflows/43?version=1, https://usegalaxy.eu/published/workflow?id=402b14906a03b2ef, https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60, https://usegalaxy.eu/published/workflow?id=941400d10c346b2c, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=bc5ced57e711acf9, https://usegalaxy.eu/published/workflow?id=d102a20c31d4673c, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.eu/published/workflow?id=e97b938ca4723827, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=b3974acb70608e38, https://usegalaxy.fr/published/workflow?id=c7be6e229a045fad, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://usegalaxy.fr/published/workflow?id=e134e9637adfc5b6, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3, https://usegalaxy.org.au/published/workflow?id=d62b6717202f42c9, https://usegalaxy.org.au/published/workflow?id=f21446cc44da50ce, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=8d8e8927d63803ef, https://usegalaxy.org/published/workflow?id=956987e628530c79, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=be54e57345ce7ca5, https://usegalaxy.org/published/workflow?id=f737593a1db217c8, https://workflowhub.eu/workflows/1260?version=1 evolution/abc_intro_phylo, genome-annotation/gene-centric, sequence-analysis/tapscan-streptophyte-algae, sequence-analysis/viral_primer_design, variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon
mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track 2014-05-19 1.0.0 To update Visualization, Convert Formats, Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
markitdown markitdown Convert documents to Markdown using markitdown 2025-04-21 https://github.com/microsoft/markitdown 0.1.1 To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/markitdown https://github.com/bgruening/galaxytools/tree/master/tools/markitdown 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mavedb_importer mavedb_importer data source for MaveDB 2023-12-13 0.9 To update Data Source bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 10 10 0 0 0 0 0 0 0 0 0 0 0 0 2 6 10 30
mea mea Maximum expected accuracy prediction 2015-07-29 http://www.bioinf.uni-leipzig.de/Software/mea 0.6.4.1 mea 0.6.4 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 5 51 86 0 0 0 0 0 0 0 0 0 0 0 0 4 13 51 188
megablast_xml_parser megablast_xml_parser Parse blast XML output 2014-05-19 1.0.1 python To update Next Gen Mappers, Convert Formats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 149 1397 1493 82 465 277 2884 0 0 0 0 0 0 0 0 189 992 1674 7725 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a
merge gops_merge_1 Merge the overlapping intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 424 458 566469 567263 650 4398 46387 108629 96 137 19795 20050 9 10 1141 1151 1179 7361 633792 1964677 https://dev.workflowhub.eu/workflows/194?version=2, https://usegalaxy.eu/published/workflow?id=06544e74f583fd05, https://usegalaxy.eu/published/workflow?id=3aaea772745ca295, https://usegalaxy.eu/published/workflow?id=522500fac247be6f, https://usegalaxy.eu/published/workflow?id=5ded4002e684a02c, https://usegalaxy.eu/published/workflow?id=6c91fe92ef069d64, https://usegalaxy.eu/published/workflow?id=7b7d6a5c6c65d74b, https://usegalaxy.eu/published/workflow?id=b8fc492025ad6ff0, https://usegalaxy.eu/published/workflow?id=c832ecfa83bcda14, https://usegalaxy.fr/published/workflow?id=0df61a88d64de252, https://usegalaxy.fr/published/workflow?id=a3e9062133fdf7c2, https://usegalaxy.fr/published/workflow?id=bf8ffe72b7ce4570, https://usegalaxy.org.au/published/workflow?id=2955ea7be1cdda29, https://usegalaxy.org.au/published/workflow?id=2b71eb1dc2aa28a1, https://usegalaxy.org.au/published/workflow?id=4b681937a01df465, https://usegalaxy.org.au/published/workflow?id=5cd7f1824db7a960, https://usegalaxy.org.au/published/workflow?id=6795e545b0cafded, https://usegalaxy.org.au/published/workflow?id=851552cc3e830253, https://usegalaxy.org.au/published/workflow?id=a77ce877e786d44a, https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886, https://usegalaxy.org.au/published/workflow?id=ebd1ee73906fdea0, https://usegalaxy.org.au/published/workflow?id=f65b54fcffaa11e5, https://usegalaxy.org/published/workflow?id=0392de36b6f55a8f, https://usegalaxy.org/published/workflow?id=31cc891be77cbc6f, https://usegalaxy.org/published/workflow?id=44b27a1296633366, https://usegalaxy.org/published/workflow?id=4ffdb2cf21759d26, https://usegalaxy.org/published/workflow?id=507c817755b2410d, https://usegalaxy.org/published/workflow?id=65f3a5772ae05a7a, https://usegalaxy.org/published/workflow?id=6ba03802169c0063, https://usegalaxy.org/published/workflow?id=7b20a62d69d53efc, https://usegalaxy.org/published/workflow?id=d136d24e4c96962a, https://usegalaxy.org/published/workflow?id=f25a3da4b00eddbb, https://usegalaxy.org/published/workflow?id=f365c53b5024d7f1, https://workflowhub.eu/workflows/138?version=5, https://workflowhub.eu/workflows/356?version=1
merge_cols mergeCols1 Merge columns together. 2012-12-04 1.0.3 python To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 1 0 1 1 1 1 1 1 1953 2236 23714 34471 865 3245 21137 134129 123 162 1605 2020 90 91 474 484 3031 11796 46930 264964 https://dev.workflowhub.eu/workflows/1113?version=2, https://dev.workflowhub.eu/workflows/1229?version=1, https://dev.workflowhub.eu/workflows/1283?version=2, https://dev.workflowhub.eu/workflows/1321?version=1, https://dev.workflowhub.eu/workflows/1363?version=1, https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.eu/published/workflow?id=14714876dda7186d, https://usegalaxy.eu/published/workflow?id=57cfe5062c8e01bf, https://usegalaxy.eu/published/workflow?id=5e09d5e991009cda, https://usegalaxy.eu/published/workflow?id=c94a1d028357c81e, https://usegalaxy.eu/published/workflow?id=d0ae255151450dad, https://usegalaxy.eu/published/workflow?id=d33ab07e4cf44f8c, https://usegalaxy.eu/published/workflow?id=f7a7c72489d6b3d4, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org.au/published/workflow?id=bdb498b1f0e8944f, https://usegalaxy.org/published/workflow?id=138311394c077827, https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe, https://usegalaxy.org/published/workflow?id=2d64e09025ae8ed4, https://usegalaxy.org/published/workflow?id=44b27a1296633366, https://usegalaxy.org/published/workflow?id=5bc973dd30f22525, https://usegalaxy.org/published/workflow?id=66748e20a243eafe, https://usegalaxy.org/published/workflow?id=68a9f03d99676bdc, https://usegalaxy.org/published/workflow?id=6c604ad86b79efab, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=8b1eedebcb94ba93, https://usegalaxy.org/published/workflow?id=941ced9f12eecd3c, https://usegalaxy.org/published/workflow?id=9864961cc6132562, https://usegalaxy.org/published/workflow?id=b8742810ac30429d, https://usegalaxy.org/published/workflow?id=c17fa637bcdec86e, https://usegalaxy.org/published/workflow?id=c3ea8fa3bb202dc6, https://usegalaxy.org/published/workflow?id=cd1badac800122c2, https://usegalaxy.org/published/workflow?id=e3e646407e3f921d, https://usegalaxy.org/published/workflow?id=e75a7802d2941f31, https://workflowhub.eu/workflows/1208?version=1 assembly/ecoli_comparison, ecology/Ecoregionalization_tutorial, ecology/PAMPA-toolsuite-tutorial, ecology/regionalGAM, transcriptomics/rna-seq-counts-to-genes
methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 124 453 530 5461 0 0 0 0 0 0 0 0 0 0 0 0 124 701 530 6521
methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. 2016-12-20 http://bioconductor.org/packages/release/bioc/html/methylKit.html 0.99.2 bioconductor-methylkit 1.32.0 To update Epigenetics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 7 7 1 3 7 21
metilene metilene Differential DNA methylation calling 2015-12-14 0.2.6.1 metilene 0.2.8 To update RNA, Statistics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 283 459 3235 4895 118 118 667 667 54 54 418 418 1 1 1 1 456 1544 4321 14623 https://dev.workflowhub.eu/workflows/1157?version=2, https://usegalaxy.eu/published/workflow?id=489926f9299594fe, https://usegalaxy.eu/published/workflow?id=bffeb3cd0c708441, https://usegalaxy.eu/published/workflow?id=c46345ba876d5bfe, https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0 epigenetics/methylation-seq
mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. 2024-05-14 https://github.com/jstjohn/SeqPrep 1.2 To update Fastq Manipulation, Sequence Analysis Nucleic acid design Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Genomics, Sequence assembly, Sequencing, Probes and primers bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 1208 1208 27 27 46 46 0 0 0 0 0 0 0 0 31 93 1254 3762 https://usegalaxy.eu/published/workflow?id=f9648091c06171cd, https://workflowhub.eu/workflows/1272?version=1
miclip mi_clip Identification of binding sites in CLIP-Seq data. 2015-02-28 https://cran.r-project.org/src/contrib/Archive/MiClip/ 1.2.0 Rscript To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments 2014-04-01 1.0.0 sputnik To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 142 118 978 0 0 0 0 0 0 0 0 50 242 118 1214
microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes 2014-04-01 1.1.0 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 89 35 315 0 0 0 0 0 0 0 0 24 137 35 385
minced minced MinCED - Mining CRISPRs in Environmental Datasets 2015-02-28 http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README 0.2.0 minced 0.4.2 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 131 143 1864 1972 0 0 0 0 0 0 0 0 0 0 0 0 131 405 1864 5700
mine maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration 2014-07-28 0.0.1 MINE To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 8 8 11 7 20 18 64 0 0 0 0 0 0 0 0 14 56 26 127
minipolish minipolish Polishing miniasm assemblies 2022-10-19 https://github.com/rrwick/Minipolish 0.1.3 minipolish 0.1.3 Up-to-date Sequence Analysis Localised reassembly, Read depth analysis Localised reassembly, Read depth analysis Sequence assembly, Sequencing Sequence assembly, Sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 35 35 251 251 0 0 0 0 0 0 0 0 0 0 0 0 35 105 251 753
mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. 2021-05-29 https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 3.2.3 To update Assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 208 208 1231 1231 118 118 723 723 30 30 597 597 0 0 0 0 356 1068 2551 7653 https://dev.workflowhub.eu/workflows/1360?version=1, https://usegalaxy.eu/published/workflow?id=2062c7e1c50b05f3, https://usegalaxy.org.au/published/workflow?id=614898119cf0dabf, https://usegalaxy.org/published/workflow?id=982a3eb2b4c4f5ae, https://workflowhub.eu/workflows/738?version=1 assembly/mitochondrion-assembly
molecule_to_gspan bg_mol2gspan converter 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
motus mereg_mOTUs_tables, motus_profiler Tool for profiling the abundance of microbial taxa. 2024-09-06 https://github.com/motu-tool/mOTUs 3.1.0 motus 3.1.0 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs https://github.com/bgruening/galaxytools/tree/master/tools/motus mOTUs Metagenomic operational taxonomic units (mOTUs) Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 76 76 0 0 0 0 0 0 0 0 0 0 0 0 12 36 76 228
mqc mqc Ribosome profiling mapping quality control tool 2017-08-11 https://github.com/Biobix/mQC 1.9 mqc 1.10 To update Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 8 9 58 76 0 0 0 0 0 0 0 0 0 0 0 0 8 25 58 192
multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites 2013-09-25 1.0.0 bx-sputnik To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mummer mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot 2014-05-22 http://mummer.sourceforge.net/ 0.0.8 ghostscript 9.18 To update Graphics, Sequence Analysis, Visualization peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 221 239 970 1030 229 229 817 817 28 49 117 202 1 1 3 3 479 1476 1907 5866
music music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) 2021-09-12 https://github.com/xuranw/MuSiC 0.1.1 music-deconvolution 0.1.1 Up-to-date Transcriptomics, Single Cell bgruening https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution music_deconvolution MuSiC Deconvolution MuSiC utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. By appropriate weighting of genes showing cross-subject and cross-cell consistency, MuSiC enables the transfer of cell type-specific gene expression information from one dataset to another. 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 313 313 4035 4035 105 105 438 438 22 22 1778 1778 0 0 0 0 440 1320 6251 18753 https://dev.workflowhub.eu/workflows/1223?version=1, https://dev.workflowhub.eu/workflows/1230?version=1, https://dev.workflowhub.eu/workflows/1234?version=2, https://dev.workflowhub.eu/workflows/1261?version=1, https://dev.workflowhub.eu/workflows/1390?version=1, https://dev.workflowhub.eu/workflows/1396?version=1, https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=2ae4a83327615155, https://usegalaxy.eu/published/workflow?id=39dd6365ff076dc4, https://usegalaxy.eu/published/workflow?id=5cbaaf2fe80b52a2, https://usegalaxy.eu/published/workflow?id=cb978151b1686b71, https://usegalaxy.eu/published/workflow?id=d1ab8eabcbe0a004 single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music, single-cell/bulk-music-2-preparescref, single-cell/bulk-music-3-preparebulk, single-cell/bulk-music-4-compare
mutate_snp_codon mutate_snp_codon_1 Mutate Codons with SNPs 2013-09-25 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5 5 34 49 18 121 52 423 0 0 0 0 0 0 0 0 23 172 86 644
nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. 2018-05-28 https://github.com/jts/nanopolish 0.14.0 nanopolish 0.14.0 Up-to-date bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 210 232 9073 9719 0 0 0 0 46 51 2470 2625 5 5 75 75 261 810 11618 35655 https://usegalaxy.eu/published/workflow?id=1cc3b4f1b50ba427, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d, https://usegalaxy.eu/published/workflow?id=816815a93cc68244, https://usegalaxy.eu/published/workflow?id=b2dfa74f55a73409, https://workflowhub.eu/workflows/50?version=1, https://workflowhub.eu/workflows/51?version=1
nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq 2017-02-21 https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ 1.0 r-nastiseq 1.0 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 2 28 42 0 0 0 0 0 0 0 0 0 0 0 0 2 6 28 98
netboxr netboxr netboxr enables automated discovery of biological process modules by network analysis 2022-08-24 1.6.0 bioconductor-netboxr 1.9.0 To update Systems Biology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/netboxr 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 13 13 0 0 0 0 0 0 0 0 0 0 0 0 6 18 13 39
nextdenovo nextdenovo String graph-based de novo assembler for long reads 2023-02-09 https://github.com/Nextomics/NextDenovo 2.5.0 nextdenovo 2.5.2 To update Assembly De-novo assembly, Genome assembly De-novo assembly, Genome assembly Sequencing, Sequence assembly Sequencing, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo nextdenovo NextDenovo NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 181 181 470 470 39 39 73 73 0 0 0 0 0 0 0 0 220 660 543 1629 https://workflowhub.eu/workflows/789?version=1
nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences 2013-04-17 http://www.moseslab.csb.utoronto.ca/NLStradamus 0.0.11 NLStradamus 1.8 To update Fasta Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
nucleosome_prediction Nucleosome Prediction of Nucleosomes Positions on the Genome 2016-09-27 https://genie.weizmann.ac.il/software/nucleo_exe.html 3.0 nucleosome_prediction 3.0 Up-to-date Sequence Analysis Prediction and recognition, Nucleosome position prediction, Sequence analysis Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Structural genomics, Nucleic acid sites, features and motifs bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 26 77 865 0 0 0 0 0 0 0 0 0 0 0 0 18 62 77 1019
numeric_clustering numeric_clustering Clustering tool for numberic values 2015-12-19 http://scikit-learn.org/stable/index.html 0.9 anaconda To update Statistics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 3 11 258 486 0 0 0 0 0 0 0 0 2 2 2 2 5 23 260 1008
openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. 2015-02-28 2.1.0 openms 3.4.1 To update Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 7 34 135 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 135 134 0 3822 5712 32773 112807 25 25 214 214 276 276 1298 1298 0 0 0 0 4123 14259 34285 182889 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https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc, https://usegalaxy.org/published/workflow?id=0775ff66d1bc04b5, https://usegalaxy.org/published/workflow?id=9865fee6c68fc201, https://usegalaxy.org/published/workflow?id=f9048d9678e21f36, https://workflowhub.eu/workflows/613?version=2 proteomics/DIA_Analysis_OSW, proteomics/DIA_lib_OSW, proteomics/database-handling, proteomics/ntails, proteomics/protein-id-oms, proteomics/protein-id-sg-ps, proteomics/protein-quant-sil
pandas_rolling_window pandas_rolling_window Rolling window calculations 2019-05-20 https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html 0.1 numpy To update Statistics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13 13 218 282 25 25 68 68 0 0 0 0 0 0 0 0 38 114 286 922
paralyzer paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. 2016-12-02 https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ 1.5 paralyzer 1.5 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24 29 311 356 0 0 0 0 0 0 0 0 0 0 0 0 24 77 311 978 https://usegalaxy.eu/published/workflow?id=a108b575b16e6cb9
partialr_square partialRsq Compute partial R square 2014-04-01 1.0.0 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 42 36 142 0 0 0 0 0 0 0 0 8 58 36 214
peakachu peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data 2018-01-30 0.2.0+galaxy1 peakachu 0.2.0 To update Sequence Analysis, RNA rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 178 204 2713 3490 0 0 0 0 0 0 0 0 0 0 0 0 178 560 2713 8916 https://dev.workflowhub.eu/workflows/1285?version=2, https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c transcriptomics/clipseq
pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns 2014-07-28 1.0.0 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 2 0 2
pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. 2023-02-02 http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ 1.6 pfam_scan 1.6 Up-to-date Sequence Analysis Protein sequence analysis Protein sequence analysis Sequence analysis Sequence analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 85 85 970 970 115 115 738 738 22 22 339 339 0 0 0 0 222 666 2047 6141 https://dev.workflowhub.eu/workflows/1324?version=3, https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930 transcriptomics/differential-isoform-expression
pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp 2014-07-28 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pgtools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history 2017-09-28 https://www.postgresql.org postgresql To update Data Export, Data Source bgruening https://github.com/bgruening/galaxytools/tools/pgtools https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pharmcat pharmcat Pharmacogenomics Clinical Annotation Tool 2022-01-28 https://pharmcat.org/ To update Variant Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 31 31 143 143 97 97 289 289 0 0 0 0 0 0 0 0 128 384 432 1296
pileometh pileometh A tool for processing bisulfite sequencing alignments 2017-02-14 https://github.com/dpryan79/MethylDackel 0.5.2 methyldackel 0.6.1 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 641 974 15143 20612 334 334 5068 5068 96 96 2898 2898 0 0 0 0 1071 3546 23109 74796 https://dev.workflowhub.eu/workflows/1157?version=2, https://usegalaxy.eu/published/workflow?id=489926f9299594fe, https://usegalaxy.eu/published/workflow?id=bffeb3cd0c708441, https://usegalaxy.eu/published/workflow?id=c46345ba876d5bfe, https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0 epigenetics/methylation-seq
pileup_interval pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases 2015-03-06 1.0.3 bx-python 0.13.0 To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 52 60 517 648 192 1568 1328 7870 21 30 767 875 0 0 0 0 265 2188 2612 14617 https://usegalaxy.org/published/workflow?id=0b3af7e9ac69a6b7
pileup_parser pileup_parser Filter pileup on coverage and SNPs 2013-08-26 https://github.com/galaxyproject/tools-devteam/ 1.0.2 perl To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 443 507 3650 3887 1233 4610 8686 52792 176 322 1909 2652 4 4 196 196 1856 9155 14441 88409 https://usegalaxy.eu/published/workflow?id=36a4646959829018, https://usegalaxy.eu/published/workflow?id=99022559adf01c4a, https://usegalaxy.org.au/published/workflow?id=83c20d8e5fd97313, https://usegalaxy.org/published/workflow?id=0b3af7e9ac69a6b7, https://usegalaxy.org/published/workflow?id=11dac9cba49be089, https://usegalaxy.org/published/workflow?id=26d2c2d51d6a7158, https://usegalaxy.org/published/workflow?id=31dea5361ec9421c, https://usegalaxy.org/published/workflow?id=34ed5c1ceeed43c1, https://usegalaxy.org/published/workflow?id=4339d5625c15ae78, https://usegalaxy.org/published/workflow?id=558c28293ec2d239, https://usegalaxy.org/published/workflow?id=578f46106f72c971, https://usegalaxy.org/published/workflow?id=58d16d45527990b7, https://usegalaxy.org/published/workflow?id=6c68099053763993, https://usegalaxy.org/published/workflow?id=7c3faadda8f89749, https://usegalaxy.org/published/workflow?id=80fa8f0fe6330b88, https://usegalaxy.org/published/workflow?id=c7aca0f5bb660907, https://usegalaxy.org/published/workflow?id=e8b1d1e5e889c986
pipmir pipmir A method to identify novel plant miRNA. 2016-11-25 https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ 0.1.0 pipmir 1.1 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 44 49 251 312 0 0 0 0 0 0 0 0 0 0 0 0 44 137 251 814
piranha piranha Piranha is a peak-caller for CLIP- and RIP-Seq data 2015-07-02 1.2.1.0 piranha 1.2.1 To update Sequence Analysis, RNA rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 94 122 1265 2094 0 0 0 0 0 0 0 0 0 0 0 0 94 310 1265 4624 https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf
platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data 2015-02-28 http://www.well.ox.ac.uk/platypus 0.0.11 platypus To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plot_from_lda plot_for_lda_output1 Draw ROC plot on "Perform LDA" output 2014-07-28 1.0.1 R To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18 25 53 77 37 348 102 903 7 10 125 155 3 3 3 3 65 516 283 1704
plotly_ml_performance_plots plotly_ml_performance_plots performance plots for machine learning problems 2018-10-11 http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics 0.4 galaxy-ml 0.10.0 To update Visualization bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 212 232 1343 1581 181 184 1257 1315 27 27 765 765 0 0 0 0 420 1283 3365 10391 https://dev.workflowhub.eu/workflows/1294?version=1, https://dev.workflowhub.eu/workflows/1331?version=3, https://usegalaxy.eu/published/workflow?id=1d55d5d20c581b16, https://usegalaxy.eu/published/workflow?id=77fa6e5a8fa3f911, https://usegalaxy.eu/published/workflow?id=fdbf1a1a584a429c, https://usegalaxy.org.au/published/workflow?id=517f947adc81a16a, https://usegalaxy.org.au/published/workflow?id=bfd7ed2abc95b53d, https://usegalaxy.org/published/workflow?id=0cf9868ebc9ec1dc, https://usegalaxy.org/published/workflow?id=728ce1ce56c4d3da statistics/classification_machinelearning, statistics/classification_regression
plotly_parallel_coordinates_plot plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly 2018-09-23 https://plot.ly/python/parallel-coordinates-plot/ 0.2 python To update Visualization bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 123 198 667 114 124 627 665 28 28 670 670 0 0 0 0 227 729 1495 4992 https://dev.workflowhub.eu/workflows/1280?version=2, https://usegalaxy.eu/published/workflow?id=83fe480cdbb70099, https://usegalaxy.eu/published/workflow?id=c15303fcc0b53df6, https://usegalaxy.org.au/published/workflow?id=92b5a29a956a3afc statistics/age-prediction-with-ml
plotly_regression_performance_plots plotly_regression_performance_plots performance plots for regression problems 2018-10-30 http://scikit-learn.org/stable/supervised_learning.html#supervised-learning 0.1 python To update Visualization bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 244 272 774 952 121 123 494 508 29 29 238 238 0 0 0 0 394 1212 1506 4710 https://dev.workflowhub.eu/workflows/1277?version=2, https://dev.workflowhub.eu/workflows/1288?version=1, https://dev.workflowhub.eu/workflows/1308?version=1, https://dev.workflowhub.eu/workflows/1328?version=1, https://usegalaxy.eu/published/workflow?id=138d4893a1d6228e, https://usegalaxy.eu/published/workflow?id=349a945e0309b3c0, https://usegalaxy.eu/published/workflow?id=4b383d13ff512687, https://usegalaxy.eu/published/workflow?id=a669986e1a5cee31, https://usegalaxy.eu/published/workflow?id=a824fb7e65a1a939, https://usegalaxy.org.au/published/workflow?id=350433eefb835f19, https://usegalaxy.org.au/published/workflow?id=65a8ac91d6ded9a2, https://usegalaxy.org.au/published/workflow?id=697945d5f9edbf39, https://usegalaxy.org.au/published/workflow?id=cebab4f1a2405a89 statistics/FNN, statistics/age-prediction-with-ml, statistics/classification_regression, statistics/regression_machinelearning
poisson2test poisson2test Poisson two-sample test 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.1 To update Statistics, Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15 17 90 121 1 140 4 562 6 8 330 389 0 0 0 0 22 209 424 1920
predictnls predictnls Python reimplementation of predictNLS for Galaxy 2013-09-23 https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
principal_component_analysis pca1 Principal Component Analysis 2014-05-19 1.0.2 rpy To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 205 254 9751 10062 573 1514 2844 8173 0 0 0 0 15 15 43 43 793 3369 12638 43554 https://usegalaxy.org/published/workflow?id=13a550ed56b56502, https://usegalaxy.org/published/workflow?id=7ca9c5203520ca7e, https://usegalaxy.org/published/workflow?id=e10859cc568da07c
protease_prediction eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. 2016-03-13 https://github.com/fabriziocosta/eden 0.9 eden 2.0 To update Sequence Analysis, Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 17 23 105 160 0 0 0 0 0 0 0 0 0 0 0 0 17 57 105 370
protein_properties bg_protein_properties Calculation of various properties from given protein sequences 2015-06-07 0.2.0 biopython 1.70 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 92 112 499 684 0 0 0 0 0 0 0 0 0 0 0 0 92 296 499 1682
proteomics_improviser proteomics_improviser Visualisation of PepXML files 2015-02-28 http://www.improviser.uni-freiburg.de/ 1.1.0.1 To update Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pubchem_rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. 2015-02-28 https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html 0.1.0 To update Data Source bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
qiime2_dbotu_q2 qiime2_dbotu_q2 q2-dbotu is a Qiime 2 plugin for performing OTU clustering 2025-03-20 https://github.com/cduvallet/q2-dbotu/tree/master 2022.11.1+galaxy0 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/qiime2_dbotu_q2/ https://github.com/bgruening/galaxytools/tree/master/tools/qiime2_dbotu_q2 qiime2 QIIME 2 QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
quality_filter qualityFilter Filter nucleotides based on quality scores 2014-04-01 1.0.1 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 62 78 724 0 0 0 0 0 0 0 0 35 132 78 880
racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. 2018-06-11 https://github.com/isovic/racon 1.5.0 racon 1.5.0 Up-to-date Sequence Analysis Genome assembly, Mapping assembly Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Whole genome sequencing, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 942 975 29815 30641 572 572 16335 16335 193 193 6569 6569 27 27 239 239 1734 5235 52958 159700 https://dev.workflowhub.eu/workflows/1107?version=1, https://dev.workflowhub.eu/workflows/1148?version=2, https://dev.workflowhub.eu/workflows/1154?version=2, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a4f50449afde4a05, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=0c421197e022f323, https://usegalaxy.org.au/published/workflow?id=1ff6aabb7e3954ac, https://usegalaxy.org.au/published/workflow?id=45e9910f46a210d8, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=bcdc5ce2ea8700fc, https://workflowhub.eu/workflows/227?version=1, https://workflowhub.eu/workflows/228?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/51?version=1, https://workflowhub.eu/workflows/563?version=1 assembly/largegenome, microbiome/plasmid-metagenomics-nanopore
rbpbench rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs 2023-12-03 https://github.com/michauhl/RBPBench 0.8.1 rbpbench 1.0.6 To update Sequence Analysis, RNA, CLIP-seq RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 109 109 0 0 0 0 0 0 0 0 0 0 0 0 8 24 109 327
rcas rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments 2017-04-13 https://github.com/BIMSBbioinfo/RCAS 1.5.4 bioconductor-rcas 1.32.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 88 102 800 1271 0 0 0 0 0 0 0 0 0 0 0 0 88 278 800 2871 https://dev.workflowhub.eu/workflows/1285?version=2, https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c transcriptomics/clipseq
rcve rcve1 Compute RCVE 2014-04-01 1.0.0 R To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 46 32 193 0 0 0 0 0 0 0 0 6 58 32 257
reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. 2015-12-09 https://github.com/chengyuan/reago-1.1 1.1 reago 1.1 Up-to-date Metagenomics, RNA Sequence assembly Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Sequence assembly, RNA, Metagenomics, Microbiology rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 3
remove_beginning Remove beginning1 Remove lines from the beginning of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 1 0 1 1 1 1 1 1 3916 4163 195233 218293 4306 8745 40935 119915 1492 1650 12870 13927 213 213 1051 1119 9927 34625 250089 853432 https://dev.workflowhub.eu/workflows/1064?version=1, https://dev.workflowhub.eu/workflows/1077?version=2, https://dev.workflowhub.eu/workflows/1083?version=1, https://dev.workflowhub.eu/workflows/1085?version=2, https://dev.workflowhub.eu/workflows/1090?version=2, https://dev.workflowhub.eu/workflows/1098?version=1, https://dev.workflowhub.eu/workflows/1145?version=1, https://dev.workflowhub.eu/workflows/1165?version=2, https://dev.workflowhub.eu/workflows/1177?version=2, 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epigenetics/ewas-suite, galaxy-interface/workflow-reports, genome-annotation/bacterial-comparative-genomics-dataset-construction, genome-annotation/secondary-metabolite-discovery, introduction/data-manipulation-olympics, introduction/galaxy-intro-101-everyone, introduction/galaxy-reproduce, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/metaquantome-data-creation, proteomics/neoantigen-3-fragpipe-discovery, proteomics/neoantigen-7-hla-binding-novel-peptides, sequence-analysis/tapscan-streptophyte-algae, single-cell/bulk-deconvolution-evaluate, statistics/classification_machinelearning, statistics/regression_machinelearning, transcriptomics/differential-isoform-expression, visualisation/circos
remurna remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation 2016-11-24 https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna 1.0.0 remurna 1.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 8 9 53 66 0 0 0 0 0 0 0 0 0 0 0 0 8 25 53 172
repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. 2015-02-28 http://www.repeatmasker.org/ 0.1.2 RepeatMasker 4.1.9 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1028 1029 7954 7965 993 993 9105 9105 352 352 3810 3810 85 85 518 518 2458 7375 21387 64172 https://dev.workflowhub.eu/workflows/1198?version=1, https://dev.workflowhub.eu/workflows/1264?version=2, https://usegalaxy.eu/published/workflow?id=09c534f738426a6d, https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a71349ba0bff403a, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=ffb1117077f68a9f, https://usegalaxy.org/published/workflow?id=effc17e170263ae6, https://usegalaxy.org/published/workflow?id=f2f633d2b02b6050, https://usegalaxy.org/published/workflow?id=fb8b997f516288e1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/575?version=1, https://workflowhub.eu/workflows/753?version=1, https://workflowhub.eu/workflows/875?version=3 ecology/phylogeny-data-prep, genome-annotation/repeatmasker
replace_column_by_key_value_file replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. 2017-02-24 0.2 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 475 527 577626 577795 277 399 42943 44495 113 113 2271 2271 11 11 2035 2035 876 2802 624875 1876346 https://dev.workflowhub.eu/workflows/1157?version=2, https://dev.workflowhub.eu/workflows/1343?version=2, https://dev.workflowhub.eu/workflows/199?version=2, https://usegalaxy.eu/published/workflow?id=036990ecf300a99f, https://usegalaxy.eu/published/workflow?id=05bd1d9c61df5d16, https://usegalaxy.eu/published/workflow?id=0c94260298199d8b, https://usegalaxy.eu/published/workflow?id=20592f292c205954, https://usegalaxy.eu/published/workflow?id=27fca972f1d1a312, https://usegalaxy.eu/published/workflow?id=2d509fad86eb97fb, https://usegalaxy.eu/published/workflow?id=37b04b02ec08e84f, https://usegalaxy.eu/published/workflow?id=6e0330de5d80e619, https://usegalaxy.eu/published/workflow?id=70ec8b1719e25982, https://usegalaxy.eu/published/workflow?id=88f5cef7e4146520, https://usegalaxy.eu/published/workflow?id=9eb29cc96d8d75c2, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://usegalaxy.eu/published/workflow?id=eb03839cc36048f5, https://usegalaxy.fr/published/workflow?id=798c8ff19825ab2c, https://usegalaxy.fr/published/workflow?id=b168a179d1b456cb, https://usegalaxy.org.au/published/workflow?id=1764bb1f506212e8, https://usegalaxy.org.au/published/workflow?id=1782d699b0166725, https://usegalaxy.org.au/published/workflow?id=5a975438c8752269, https://usegalaxy.org.au/published/workflow?id=7a0b3968968c5994, https://usegalaxy.org.au/published/workflow?id=7cc2b5010c56f117, https://usegalaxy.org.au/published/workflow?id=800d28ec61b15244, https://usegalaxy.org.au/published/workflow?id=8e2b94c6fbf44368, https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0, https://usegalaxy.org.au/published/workflow?id=989eb73372135796, https://usegalaxy.org.au/published/workflow?id=b601f48ecec15bf4, https://usegalaxy.org.au/published/workflow?id=b920b02a23f94d11, https://usegalaxy.org.au/published/workflow?id=d0d6743450e5060d, https://usegalaxy.org.au/published/workflow?id=fbc732db2a2821b0, https://usegalaxy.org/published/workflow?id=07e761b2501971c6, https://usegalaxy.org/published/workflow?id=2967ef82911f2cca, https://usegalaxy.org/published/workflow?id=2b09f3c9465ee054, https://usegalaxy.org/published/workflow?id=2dceaa255cc8cf83, https://usegalaxy.org/published/workflow?id=6c2bb2209aad5e44, https://usegalaxy.org/published/workflow?id=7af656b8ea5e7e2e, https://usegalaxy.org/published/workflow?id=8a01c78688beae1d, https://usegalaxy.org/published/workflow?id=dcbc71347300822d, https://usegalaxy.org/published/workflow?id=f58c90061c31bd48, https://usegalaxy.org/published/workflow?id=ff3ade25b35f4893, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/109?version=9 epigenetics/methylation-seq, single-cell/scatac-standard-processing-snapatac2
ribotaper ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. 2016-06-07 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ 1.3.1a ribotaper 1.3.1 To update RNA Gene expression profiling Gene expression profiling Functional genomics Functional genomics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 80 85 630 740 0 0 0 0 0 0 0 0 0 0 0 0 80 245 630 2000
rmap rmap_wrapper RMAP for Solexa Short Reads Alignment 2014-05-19 1.0.0 rmap 2.1 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores 2014-05-19 1.0.0 rmap 2.1 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rnabob rbc_rnabob Fast pattern searching for RNA structural motifs 2015-02-28 http://eddylab.org/software.html 2.2.1.0 rnabob 2.2.1 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9 12 77 198 0 0 0 0 0 0 0 0 0 0 0 0 9 30 77 352
rnacode rbc_rnacode Analyze the protein coding potential in MSA 2015-06-16 0.3.2 rnacode 0.3 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 28 35 834 1363 0 0 0 0 0 0 0 0 0 0 0 0 28 91 834 3031 https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1
rnacommender rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. 2016-05-31 https://github.com/gianlucacorrado/RNAcommender 0.1.1 sam 3.5 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 19 22 53 1082 0 0 0 0 0 0 0 0 0 0 0 0 19 60 53 1188
rnaformer infer_rnaformer RNAformer: RNA secondary structure prediction 2024-07-11 https://github.com/automl/RNAformer 1.2.0 rnaformer To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 76 76 0 0 0 0 0 0 0 0 0 0 0 0 16 48 76 228
rnalien RNAlien RNAlien unsupervized RNA family model construction 2017-03-07 http://rna.tbi.univie.ac.at/rnalien/ 1.3.6 rnalien 1.8.0 To update RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9 14 22 33 0 0 0 0 0 0 0 0 0 0 0 0 9 32 22 77 https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1
rnashapes RNAshapes Compute secondary structures of RNA 2015-02-28 3.3.0 @EXECUTABLE@ To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 44 55 213 258 0 0 0 0 0 0 0 0 0 0 0 0 44 143 213 684
rnasnp rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs 2016-11-24 http://rth.dk/resources/rnasnp/ 1.2.0 rnasnp 1.2 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 17 21 63 95 0 0 0 0 0 0 0 0 0 0 0 0 17 55 63 221
rnaz rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. 2015-02-28 https://www.tbi.univie.ac.at/~wash/RNAz/ 2.1.1 rnaz 2.1.1 Up-to-date RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 89 125 1084 43319 0 0 0 0 0 0 0 0 0 0 0 0 89 303 1084 45487 https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1
rrna meta_rna Identification of ribosomal RNA genes in metagenomic fragments. 2015-02-28 http://weizhong-lab.ucsd.edu/meta_rna/ 0.1 hmmsearch3.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
run_jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy 2021-12-11 0.0.1 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 33 33 0 0 0 0 0 0 0 0 0 0 0 0 3 9 33 99
sailfish sailfish Sailfish is a tool for transcript quantification from RNA-seq data 2015-02-28 http://www.cs.cmu.edu/~ckingsf/software/sailfish/ 0.10.1.1 bzip2 To update Sequence Analysis, RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 178 227 3778 4615 558 1202 8794 15475 145 177 2710 3100 2 2 57 57 883 3374 15339 53925 https://usegalaxy.org/published/workflow?id=53834a5fb46ca0f6, https://usegalaxy.org/published/workflow?id=6dada297572d77bd
salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. 2016-03-21 https://github.com/COMBINE-lab/salmon 1.10.1 salmon 1.10.3 To update Sequence Analysis, RNA, Transcriptomics, Single Cell Sequence composition calculation, RNA-Seq quantification, Gene expression analysis Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics RNA-Seq, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data 2 3 3 2 0 0 0 0 0 0 0 0 0 0 0 0 3 1 0 0 0 0 0 0 2 0 0 0 0 0 3 3 3 0 2473 2597 76174 82244 3321 5029 94398 134333 509 606 14122 17236 139 139 1263 1264 6442 21255 185957 606991 https://dev.workflowhub.eu/workflows/1024?version=1, https://dev.workflowhub.eu/workflows/1025?version=1, https://dev.workflowhub.eu/workflows/1263?version=1, https://dev.workflowhub.eu/workflows/1279?version=1, https://dev.workflowhub.eu/workflows/1318?version=2, https://usegalaxy.eu/published/workflow?id=0d6bed63a2e4c3d6, https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=1ffc058273ab357e, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414, https://usegalaxy.eu/published/workflow?id=65aed668233d5f73, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37, https://usegalaxy.eu/published/workflow?id=9ed36a6849fa2014, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org.au/published/workflow?id=13a2c5bd07705985, https://usegalaxy.org.au/published/workflow?id=3f45685df9b9e792, https://usegalaxy.org.au/published/workflow?id=954318db8c8d9219, https://usegalaxy.org.au/published/workflow?id=b0614274c66efa95, https://usegalaxy.org/published/workflow?id=07fdeadce7a6d5cb, https://usegalaxy.org/published/workflow?id=08bdcecd1cb0bda3, https://usegalaxy.org/published/workflow?id=092be3cf6e40282c, https://usegalaxy.org/published/workflow?id=0930f955bdac93e8, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=228ae7f537a60226, https://usegalaxy.org/published/workflow?id=427fce51fd9508eb, https://usegalaxy.org/published/workflow?id=43c39bc86399188f, https://usegalaxy.org/published/workflow?id=5203bc68df3cf819, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=82681bd5f059e39a, https://usegalaxy.org/published/workflow?id=93650de42fb8c015, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=b1b75a9323d25085, https://usegalaxy.org/published/workflow?id=c2c6779a8b1821e0, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=dec0cf06fa059e65 single-cell/scrna-case_alevin, transcriptomics/mirna-target-finder, transcriptomics/srna
sam2interval sam2interval Convert SAM to interval. 2013-08-26 1.0.2 python To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 60 66 1280 1388 159 1751 2017 18324 10 17 534 650 3 3 3 3 232 2301 3834 28033 https://usegalaxy.org/published/workflow?id=0115daec07bb1da6, https://usegalaxy.org/published/workflow?id=02c9244e2fb060de, https://usegalaxy.org/published/workflow?id=4b52f6a8dcfc8045, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=c6a3b066c3072e4a
sam_bitwise_flag_filter sam_bw_filter Filter SAM on bitwise flag values 2013-08-26 1.0.1 python To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6 26 21 278 322 6351 2389 76050 15 29 228 365 2 2 24 24 345 7098 2662 82041 https://usegalaxy.eu/published/workflow?id=4412f7223a557b48, https://usegalaxy.org/published/workflow?id=0017c434354b6f6a, https://usegalaxy.org/published/workflow?id=055eb85c8ecf0ca3, https://usegalaxy.org/published/workflow?id=07739fbbd53755f6, https://usegalaxy.org/published/workflow?id=165c8a58baffe64c, https://usegalaxy.org/published/workflow?id=1b385fd45ee48614, https://usegalaxy.org/published/workflow?id=1e2e064c33b9c521, https://usegalaxy.org/published/workflow?id=26d2c2d51d6a7158, https://usegalaxy.org/published/workflow?id=2b3970d9b28810a1, https://usegalaxy.org/published/workflow?id=34ed5c1ceeed43c1, https://usegalaxy.org/published/workflow?id=3696bd8abe0f7746, https://usegalaxy.org/published/workflow?id=378159d1ad2e98f9, https://usegalaxy.org/published/workflow?id=38f5ab09779a6495, https://usegalaxy.org/published/workflow?id=4a5730954d776cb2, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=555e68f5c807ff73, https://usegalaxy.org/published/workflow?id=578f46106f72c971, https://usegalaxy.org/published/workflow?id=6172b57f4c49e364, https://usegalaxy.org/published/workflow?id=6f436066dffbc37d, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=83fbcdf3e29c41d0, https://usegalaxy.org/published/workflow?id=84aa86200ff74b4a, https://usegalaxy.org/published/workflow?id=92a233e5f2405830, https://usegalaxy.org/published/workflow?id=99e754eaabd7f362, https://usegalaxy.org/published/workflow?id=a23bf4cd3bc97f2a, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=b2176abeb937f026, https://usegalaxy.org/published/workflow?id=b4bb2c7d8c7b5139, https://usegalaxy.org/published/workflow?id=b4dda054d2cf15b7, https://usegalaxy.org/published/workflow?id=b72edafe11293d93, https://usegalaxy.org/published/workflow?id=c4a1246974f279c5, https://usegalaxy.org/published/workflow?id=c6a3b066c3072e4a, https://usegalaxy.org/published/workflow?id=c7aca0f5bb660907, https://usegalaxy.org/published/workflow?id=ca5ca2f38c1719e1, https://usegalaxy.org/published/workflow?id=e35ac40c58953f74, https://usegalaxy.org/published/workflow?id=e8b1d1e5e889c986, https://usegalaxy.org/published/workflow?id=ea817818a6de77e0, https://usegalaxy.org/published/workflow?id=eb20150175a6ab03, https://usegalaxy.org/published/workflow?id=f3983646b6df24bf
sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort Sambamba: process your BAM data faster! 2016-06-23 https://github.com/biod/sambamba 1.0.1 sambamba 1.0.1 Up-to-date SAM bgruening https://github.com/biod/sambamba https://github.com/bgruening/galaxytools/tree/master/tools/sambamba 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 160 160 2714 2714 0 0 0 0 0 0 0 0 0 0 0 0 160 480 2714 8142 https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1164?version=2
sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) 2014-02-18 https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 To update Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 350 404 3534 4071 166 166 1426 1426 24 24 1697 1697 9 9 113 113 549 1701 6770 20847 transcriptomics/mirna-target-finder
samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) 2014-04-14 http://www.htslib.org/ 0.0.5 samtools 1.22 To update Assembly, SAM, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
samtools_depth samtools_depth Coverage depth via samtools 2014-11-19 http://www.htslib.org/ 0.0.3 samtools 1.22 To update Assembly, Sequence Analysis, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 839 865 7380 7615 1636 1701 10500 10826 55 55 428 428 71 71 109 109 2601 7894 18417 55812 https://dev.workflowhub.eu/workflows/1083?version=1, https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8, https://usegalaxy.eu/published/workflow?id=64abcddeb516a712, https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f, https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad, https://usegalaxy.org.au/published/workflow?id=38f57cffaeb0e39f, https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba, https://usegalaxy.org/published/workflow?id=06d6dcd2655592af, https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6, https://usegalaxy.org/published/workflow?id=3f2d1003ff959c7c, https://usegalaxy.org/published/workflow?id=6d778eeb176d563c, https://usegalaxy.org/published/workflow?id=71f8a4090877f171, https://usegalaxy.org/published/workflow?id=8daa91d54040ba95, https://usegalaxy.org/published/workflow?id=b561d3d9645a2726, https://usegalaxy.org/published/workflow?id=c4af6c5f5dfaae82, https://usegalaxy.org/published/workflow?id=f3ed710e251833a7, https://workflowhub.eu/workflows/1063?version=3 microbiome/pathogen-detection-from-nanopore-foodborne-data
samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) 2013-11-11 http://www.htslib.org/ 0.0.6 samtools 1.22 To update Assembly, Next Gen Mappers, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 4479 5091 58483 62721 7420 10891 79415 118342 1280 1525 16552 17651 447 447 2609 2609 13626 45206 157059 515441 https://dev.workflowhub.eu/workflows/1150?version=2, https://dev.workflowhub.eu/workflows/1153?version=2, https://dev.workflowhub.eu/workflows/1175?version=2, https://dev.workflowhub.eu/workflows/1295?version=1, https://dev.workflowhub.eu/workflows/1299?version=2, https://dev.workflowhub.eu/workflows/1329?version=5, https://dev.workflowhub.eu/workflows/574?version=1, https://usegalaxy.eu/published/workflow?id=1089e5c66dbcc1a3, 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scatterplot scatterplot_rpy Scatterplot of two numeric columns 2014-07-28 1.0.3 numpy To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 280 1136 1838 213 1950 725 9362 0 18 0 49 14 14 41 41 416 3094 1902 15094 https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.org/published/workflow?id=857db984ff571191
sed_wrapper sed_stream_editor Manipulate your data with the sed command line tool. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed https://github.com/bgruening/galaxytools/tree/master/tools/sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 53 115 2284 0 0 0 0 0 0 0 0 0 0 0 0 9 71 115 2514 https://usegalaxy.eu/published/workflow?id=04dbf1e548db74fd, https://usegalaxy.eu/published/workflow?id=c94a1d028357c81e, https://usegalaxy.eu/published/workflow?id=f7a7c72489d6b3d4
segemehl segemehl segemehl - short read mapping with gaps 2015-02-28 http://www.bioinf.uni-leipzig.de/Software/segemehl/ 0.2.0.4 segemehl 0.3.4 To update Next Gen Mappers rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 95 115 1001 1308 0 0 0 0 0 0 0 0 0 0 0 0 95 305 1001 3310
selectsequencesfrommsa selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format 2017-03-11 https://github.com/eggzilla/SelectSequences 1.0.5 selectsequencesfrommsa 1.0.5 Up-to-date RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 42 51 272 473 0 0 0 0 0 0 0 0 0 0 0 0 42 135 272 1017 https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1
seq_composition seq_composition Sequence composition 2014-08-12 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 163 222 1224 1358 234 234 759 759 0 0 0 0 2 2 45 45 399 1256 2028 6218 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=9275d0c90a8713d6
seq_filter_by_id seq_filter_by_id Filter sequences by ID 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 786 880 31030 33625 690 692 29316 39481 166 166 3249 3249 26 26 954 954 1668 5100 64549 206407 https://dev.workflowhub.eu/workflows/1274?version=2, https://dev.workflowhub.eu/workflows/1397?version=1, https://usegalaxy.eu/published/workflow?id=3280dc48d768b46a, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=4a39d38fde81e35d, https://usegalaxy.eu/published/workflow?id=513389e1a8c6bba9, https://usegalaxy.eu/published/workflow?id=57d3109f32defa3b, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=889f2782ad82bd69, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264, https://usegalaxy.eu/published/workflow?id=d7aa4c258e2edc95, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org.au/published/workflow?id=470eb26144325590, https://usegalaxy.org.au/published/workflow?id=a1b97364f84022cf, https://usegalaxy.org/published/workflow?id=3c7349268d74c576, https://workflowhub.eu/workflows/655?version=1, https://workflowhub.eu/workflows/878?version=1 ecology/Obitools-metabarcoding, single-cell/scrna-umis
seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files 2014-11-04 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 To update Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 184 221 4363 4832 0 0 0 0 0 0 0 0 0 0 0 0 184 589 4363 13558 https://usegalaxy.eu/published/workflow?id=9668976304efea5c
seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) 2018-05-08 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 To update Fasta Manipulation, Fastq Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
seq_primer_clip seq_primer_clip Trim off 5' or 3' primers 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 To update Assembly, Fasta Manipulation, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
seq_rename seq_rename Rename sequences with ID mapping from a tabular file 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
seq_select_by_id seq_select_by_id Select sequences by ID 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 264 295 2355 3744 10 12 434 483 274 855 2789 9805
short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads 2014-05-19 1.0.0 rpy To update Sequence Analysis, Graphics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
short_reads_figure_score quality_score_distribution Build base quality distribution 2014-05-19 1.0.2 fontconfig To update Sequence Analysis, Graphics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25 30 123 163 11 711 125 3360 0 0 0 0 0 0 0 0 36 813 248 4019
short_reads_trim_seq trim_reads Select high quality segments 2014-05-19 1.0.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 44 60 134 220 54 1602 242 6657 0 0 0 0 0 0 0 0 98 1858 376 7629 https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c
show_beginning Show beginning1 Select lines from the beginning of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 0 1 1 0 0 0 1 1 0 1 0 1 1 1 1 1 1 2238 3054 79660 89440 4209 19273 18641 88049 408 499 2924 3461 135 135 503 605 6990 36941 101728 385011 https://dev.workflowhub.eu/workflows/1090?version=2, https://dev.workflowhub.eu/workflows/1206?version=1, https://dev.workflowhub.eu/workflows/1336?version=2, https://usegalaxy.eu/published/workflow?id=04b838103aed1929, https://usegalaxy.eu/published/workflow?id=1ac5745645634825, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=272e9106e50c9fe6, https://usegalaxy.eu/published/workflow?id=29346872085adf1f, https://usegalaxy.eu/published/workflow?id=2f7149d02db43b7b, 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https://workflowhub.eu/workflows/1078?version=1, https://workflowhub.eu/workflows/1260?version=1 data-science/data-manipulation-olympics, galaxy-interface/workflow-editor, introduction/data-manipulation-olympics, single-cell/scatac-batch-correction-snapatac2, transcriptomics/rna-seq-analysis-clustering-viz, variant-analysis/aiv-analysis
show_tail Show tail1 Select lines from the end of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 0 1 1 0 0 0 1 1 0 1 0 1 1 1 1 1 1 376 615 1668 2770 720 1931 10725 24885 73 93 359 487 13 14 22 42 1182 5017 12774 53732 https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, https://usegalaxy.org/published/workflow?id=427fce51fd9508eb, https://usegalaxy.org/published/workflow?id=7ca9c5203520ca7e, https://usegalaxy.org/published/workflow?id=e10859cc568da07c, https://usegalaxy.org/published/workflow?id=f806893fbe065406
sicer peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions 2014-01-27 https://home.gwu.edu/~wpeng/Software.htm 1.1 SICER 1.1 Up-to-date ChIP-seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 29 44 224 382 137 1014 791 9062 5 7 648 765 2 2 3 3 173 1413 1666 13544
sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn 2016-05-02 http://scikit-learn.org 1.0.11.0 To update Machine Learning, Statistics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 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snpfreq hgv_snpFreq snpFreq significant SNPs in case-control data 2014-07-28 1.0.1 R To update Variant Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10 12 28 44 67 185 286 657 13 23 225 279 0 0 0 0 90 400 539 2058
sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. 2015-02-28 http://bioinfo.lifl.fr/RNA/sortmerna/ 4.3.6 sortmerna 4.3.7 To update RNA Sequence similarity search, Sequence comparison, Sequence alignment analysis Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics Metatranscriptomics, Metagenomics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1115 1215 21173 22817 437 437 5232 5232 198 198 3453 3453 96 96 561 564 1846 5638 30419 92904 https://dev.workflowhub.eu/workflows/1092?version=1, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.eu/published/workflow?id=f6e8a63283262518, https://usegalaxy.eu/published/workflow?id=fd90652d475ed739, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.org.au/published/workflow?id=408a31694e9c85e6 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short
split_file_on_column tp_split_on_column Split a file on a specific column. 2015-02-28 0.6 gawk To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 463 517 6473 6789 349 349 2601 2601 10 10 143 143 25 25 36 36 847 2595 9253 28075 https://dev.workflowhub.eu/workflows/1077?version=2, https://dev.workflowhub.eu/workflows/1090?version=2, https://dev.workflowhub.eu/workflows/1173?version=2, https://dev.workflowhub.eu/workflows/1206?version=1, https://dev.workflowhub.eu/workflows/1365?version=1, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1f3f6757de60d3cf, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=39dd6365ff076dc4, https://usegalaxy.eu/published/workflow?id=5f053303601cc630, https://usegalaxy.eu/published/workflow?id=739214a6dfa194e1, https://usegalaxy.eu/published/workflow?id=7c80cd57b2de54d4, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=933ab5e7fe13a8e0, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=e87e726b57f1a875, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=7a0b3968968c5994, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=2967ef82911f2cca, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=fbf75fbb72b488bd, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1189?version=2 data-science/data-manipulation-olympics, genome-annotation/gene-centric, imaging/parameter-tuning, introduction/data-manipulation-olympics, microbiome/pathogen-detection-from-nanopore-foodborne-data, single-cell/GO-enrichment
split_file_to_collection split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. 2018-07-10 https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.2 python To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 1096 1127 18554 19049 757 757 10070 10070 167 167 4645 4645 32 32 685 685 2052 6187 33954 102357 https://dev.workflowhub.eu/workflows/1079?version=2, https://dev.workflowhub.eu/workflows/1082?version=2, https://dev.workflowhub.eu/workflows/1091?version=1, https://dev.workflowhub.eu/workflows/1367?version=1, https://dev.workflowhub.eu/workflows/1395?version=1, https://dev.workflowhub.eu/workflows/193?version=2, 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sshmm sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data 2018-07-05 https://github.molgen.mpg.de/heller/ssHMM 1.0.7 sshmm 1.0.7 Up-to-date Sequence Analysis, RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 17 20 198 227 0 0 0 0 0 0 0 0 0 0 0 0 17 54 198 623
stats_perf_tool stats_perf_tool suitable for boolean classification problems 2015-02-28 http://osmot.cs.cornell.edu/kddcup/software.html 5.11.0 perf To update bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf https://github.com/bgruening/galaxytools/tree/master/tools/perf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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substitution_rates subRate1 Estimate substitution rates for non-coding regions 2014-04-01 1.0.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 747 101 3901 3 4 88 114 0 0 0 0 37 825 189 4393
substitutions substitutions1 Fetch substitutions from pairwise alignments 2014-04-01 1.0.1 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 84 74 901 0 0 0 0 0 0 0 0 13 110 74 1049
subtract gops_subtract_1 Subtract the intervals of two datasets 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 413 481 566951 567726 1348 7676 49053 185201 132 189 20589 21010 8 9 1135 1145 1901 12157 637728 2050538 https://dev.workflowhub.eu/workflows/194?version=2, https://usegalaxy.eu/published/workflow?id=06544e74f583fd05, https://usegalaxy.eu/published/workflow?id=3aaea772745ca295, https://usegalaxy.eu/published/workflow?id=522500fac247be6f, https://usegalaxy.eu/published/workflow?id=5ded4002e684a02c, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=6c91fe92ef069d64, https://usegalaxy.eu/published/workflow?id=7b7d6a5c6c65d74b, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.eu/published/workflow?id=b8fc492025ad6ff0, https://usegalaxy.eu/published/workflow?id=c832ecfa83bcda14, https://usegalaxy.fr/published/workflow?id=0df61a88d64de252, https://usegalaxy.fr/published/workflow?id=a3e9062133fdf7c2, https://usegalaxy.fr/published/workflow?id=bf8ffe72b7ce4570, https://usegalaxy.org.au/published/workflow?id=2955ea7be1cdda29, https://usegalaxy.org.au/published/workflow?id=2b71eb1dc2aa28a1, https://usegalaxy.org.au/published/workflow?id=4b681937a01df465, https://usegalaxy.org.au/published/workflow?id=5cd7f1824db7a960, https://usegalaxy.org.au/published/workflow?id=6795e545b0cafded, https://usegalaxy.org.au/published/workflow?id=851552cc3e830253, https://usegalaxy.org.au/published/workflow?id=a77ce877e786d44a, https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886, https://usegalaxy.org.au/published/workflow?id=ebd1ee73906fdea0, https://usegalaxy.org.au/published/workflow?id=f65b54fcffaa11e5, https://usegalaxy.org/published/workflow?id=0392de36b6f55a8f, https://usegalaxy.org/published/workflow?id=31cc891be77cbc6f, https://usegalaxy.org/published/workflow?id=4ffdb2cf21759d26, https://usegalaxy.org/published/workflow?id=507c817755b2410d, https://usegalaxy.org/published/workflow?id=65f3a5772ae05a7a, https://usegalaxy.org/published/workflow?id=66748e20a243eafe, https://usegalaxy.org/published/workflow?id=6ba03802169c0063, https://usegalaxy.org/published/workflow?id=7b20a62d69d53efc, https://usegalaxy.org/published/workflow?id=7bc71a005c6f18d0, https://usegalaxy.org/published/workflow?id=b1cd3f793187d667, https://usegalaxy.org/published/workflow?id=d136d24e4c96962a, https://usegalaxy.org/published/workflow?id=f365c53b5024d7f1, https://workflowhub.eu/workflows/138?version=5, https://workflowhub.eu/workflows/356?version=1
subtract_query subtract_query1 Subtract Whole Dataset from another dataset 2014-04-01 https://github.com/galaxyproject/gops 0.1 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 127 149 1149 1479 606 3463 2932 40656 25 39 796 1035 15 17 103 125 773 5214 4980 53255 https://usegalaxy.eu/published/workflow?id=82ef590b5821805d, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.org/published/workflow?id=0115daec07bb1da6, https://usegalaxy.org/published/workflow?id=a3de4b3f7b910059, https://usegalaxy.org/published/workflow?id=b2176abeb937f026
sylph sylph_profile, sylph_query sylph - fast and precise species-level metagenomic profiling with ANIs 2024-10-08 https://github.com/bluenote-1577/sylph 0.8.1 sylph 0.8.1 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics bgruening https://github.com/bgruening/galaxytools/main/tools/sylph https://github.com/bgruening/galaxytools/tree/master/tools/sylph sylph sylph fast and precise species-level metagenomic profiling with ANIs 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
t2ps Draw_phylogram Draw phylogeny 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.1 To update Metagenomics Phylogenetic tree visualisation Phylogenetic tree visualisation Phylogenomics Phylogenomics devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps t2ps Draw phylogeny "Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format." - Galaxy tool wrapper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 67 92 411 478 13 1240 102 7952 0 0 0 0 0 0 0 0 80 1492 513 9456 https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c
t2t_report t2t_report Summarize taxonomy 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.1 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 63 79 915 960 17 1143 127 7194 0 0 0 0 0 0 0 0 80 1382 1042 10238 https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c
t_test_two_samples t_test_two_samples T Test for Two Samples 2013-09-25 1.0.1 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20 32 102 218 77 283 404 1193 11 12 1037 1244 3 3 4 4 111 552 1547 5753
table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered 2013-12-02 0.2 annovar To update Variant Analysis devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2438 7461 13993 64533 0 0 0 0 0 0 0 0 2438 12337 13993 92519 https://usegalaxy.org/published/workflow?id=02755c14619242da, https://usegalaxy.org/published/workflow?id=049e6609da2b67c4, https://usegalaxy.org/published/workflow?id=0660a00407fc16a1, https://usegalaxy.org/published/workflow?id=0843c6f15eae2f15, https://usegalaxy.org/published/workflow?id=0a89328e6d28dd07, https://usegalaxy.org/published/workflow?id=0d8eb75d28fa7df2, https://usegalaxy.org/published/workflow?id=10d8d47f97afc999, https://usegalaxy.org/published/workflow?id=17a7ff756d37a437, 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tables_arithmetic_operations tables_arithmetic_operations Arithmetic Operations on tables 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 perl To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 32 39 2130 2221 0 0 0 0 0 0 0 0 4 5 79 89 36 116 2209 6728 https://workflowhub.eu/workflows/789?version=1
tabpfn tabpfn Tabular data prediction using TabPFN using Pytorch. 2024-10-14 https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn 2.0.9 tabpfn To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 73 73 0 0 0 0 0 0 0 0 0 0 0 0 2 6 73 219
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proteomics/proteogenomics-dbsearch, sequence-analysis/Manage_AB1_Sanger
tapscan tapscan_classify Search for transcription associated proteins (TAPs) 2024-02-14 https://plantcode.cup.uni-freiburg.de/tapscan/ 4.76+galaxy0 hmmer 3.4 To update Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 38 38 0 0 0 0 0 0 0 0 0 0 0 0 9 27 38 114 sequence-analysis/tapscan-streptophyte-algae
targetfinder targetfinder Plant small RNA target prediction tool 2015-10-23 https://github.com/carringtonlab/TargetFinder.git 1.7 targetfinder 1.7 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 99 102 864 885 59 59 258 258 33 33 1069 1069 0 0 0 0 191 576 2191 6594 https://dev.workflowhub.eu/workflows/1318?version=2, https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50 transcriptomics/mirna-target-finder
text_processing tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. 2015-02-28 https://www.gnu.org/software/ 9.5 coreutils 8.25 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 20 20 20 20 0 0 0 0 0 0 0 0 0 0 0 19 1 19 0 0 0 0 0 0 20 0 0 0 0 0 19 20 19 0 40814 46899 4100067 4232269 48946 75060 683504 992986 8269 8636 123207 126732 1986 1987 26461 26494 100015 332612 4933239 15244959 https://dev.workflowhub.eu/workflows/1002?version=1, 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tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. 2021-11-14 https://github.com/BGI-Qingdao/TGS-GapCloser 1.0.3 tgsgapcloser 1.2.1 To update Assembly Genome assembly, Read mapping, Scaffolding, Localised reassembly Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 53 53 552 552 0 0 0 0 0 0 0 0 0 0 0 0 53 159 552 1656
tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. 2024-05-23 https://github.com/ibe-uw/tiara 1.0.3 tiara To update Metagenomics, Sequence Analysis Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation Sequencing, Genomics, DNA polymorphism bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 296 296 0 0 0 0 0 0 0 0 0 0 0 0 16 48 296 888
tmhmm_and_signalp promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb 2010-10-21 https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 1244 1422 12344 13651 1 1 2 2 0 0 0 0 0 2 0 6 1245 3915 12346 38351 https://dev.workflowhub.eu/workflows/1035?version=1, https://dev.workflowhub.eu/workflows/1143?version=2, https://usegalaxy.eu/published/workflow?id=3280dc48d768b46a, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://usegalaxy.eu/published/workflow?id=cde27d06b74ad2fd proteomics/secretome-prediction
tophat tophat Tophat for Illumina 2014-01-27 1.5.0 samtools 1.22 To update RNA, Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 24 7228 123 66524 0 0 0 0 0 0 0 0 24 7277 123 66771 https://usegalaxy.org/published/workflow?id=035c28a247976f2c, https://usegalaxy.org/published/workflow?id=0599241ce8eae217, https://usegalaxy.org/published/workflow?id=0769f77979798f16, https://usegalaxy.org/published/workflow?id=0bddfc0618e59d02, https://usegalaxy.org/published/workflow?id=3686146fc097c66f, https://usegalaxy.org/published/workflow?id=41b181f1d763e419, https://usegalaxy.org/published/workflow?id=462261c5e22635f0, https://usegalaxy.org/published/workflow?id=46f8999f91221fed, https://usegalaxy.org/published/workflow?id=486ee20613d58dcf, https://usegalaxy.org/published/workflow?id=61b7ad6588f7db41, https://usegalaxy.org/published/workflow?id=62401f33a369bac0, https://usegalaxy.org/published/workflow?id=684ff8ee49c7f116, https://usegalaxy.org/published/workflow?id=69bb44cd732a0c49, https://usegalaxy.org/published/workflow?id=712d9ae42b45c4b9, https://usegalaxy.org/published/workflow?id=7253824f78a90431, https://usegalaxy.org/published/workflow?id=77e4bb9d6aea0c9a, https://usegalaxy.org/published/workflow?id=7c3b5398dd05a6a5, https://usegalaxy.org/published/workflow?id=a24092b7f00b4e2a, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=b5c79535c499bc58, https://usegalaxy.org/published/workflow?id=eae740bac11ecc91, https://usegalaxy.org/published/workflow?id=fcce98489c8ca7a3
tophat2 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads 2014-01-27 http://ccb.jhu.edu/software/tophat/index.shtml 2.1.1 bowtie2 2.5.4 To update RNA, Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 1038 1759 14952 27721 7697 28159 75300 345961 393 1035 4936 14370 0 0 0 0 9128 49209 95188 578428 https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=60f2a8721e203057, https://usegalaxy.eu/published/workflow?id=eb3cfa4d1f05fc0e, https://usegalaxy.org.au/published/workflow?id=0427bd5f28789a1f, https://usegalaxy.org.au/published/workflow?id=115896e8f4059e44, https://usegalaxy.org.au/published/workflow?id=126116a92f2e9a68, 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tophat_fusion_post tophat_fusion_post Wrapper for Tophat-Fusion post step 2014-01-27 0.1 blast+ To update Transcriptomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 39 48 209 249 2 191 6 814 7 12 95 120 0 0 0 0 48 347 310 1803
trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer 2015-02-28 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ 0.6.10 trim-galore 0.6.10 Up-to-date Sequence Analysis, Fastq Manipulation Sequence trimming, Primer removal, Read pre-processing Sequence trimming, Primer removal, Read pre-processing Sequence analysis Sequence analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5968 7091 267020 328827 12187 17960 260025 373545 1474 1684 31547 33788 255 255 2790 2790 19884 66758 561382 1861714 https://dev.workflowhub.eu/workflows/1152?version=2, 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transcriptomics/srna, variant-analysis/baculovirus-isolate-variation
trimmer trimmer Trim leading or trailing characters. 2012-12-04 0.0.1 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 1 0 1 1 1 1 1 1 544 628 5722 8055 619 2986 14579 109059 62 91 572 1140 10 11 36 56 1235 6186 20909 160128 https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5, https://usegalaxy.eu/published/workflow?id=250e6058f160825f, https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09, https://usegalaxy.eu/published/workflow?id=7c80cd57b2de54d4, https://usegalaxy.eu/published/workflow?id=933ab5e7fe13a8e0, https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://usegalaxy.org/published/workflow?id=08edef22fa132799, https://usegalaxy.org/published/workflow?id=0a3513961f0cf9dd, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=3269026bb1e0ec42, https://usegalaxy.org/published/workflow?id=3edea70fbdb9dbd9, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=7ca9c5203520ca7e, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://usegalaxy.org/published/workflow?id=e107d8036c064616, https://usegalaxy.org/published/workflow?id=e10859cc568da07c, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22
trna_prediction aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. 2015-02-28 http://mbioserv2.mbioekol.lu.se/ARAGORN/ 0.6 aragorn 1.2.41 To update RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 0 803 945 5108 5535 0 0 0 0 220 220 2718 2718 0 0 0 0 1023 3211 7826 23905 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=9275d0c90a8713d6, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178
ucsc_custom_track build_ucsc_custom_track_1 Build custom track for UCSC genome browser 2014-07-28 1.0.1 python To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 144 165 424 529 609 4139 2248 18852 0 0 0 0 0 1 0 10 753 5811 2672 24735 https://usegalaxy.eu/published/workflow?id=0ed8817a90caa2b1, https://usegalaxy.eu/published/workflow?id=7878623b7e959284, https://usegalaxy.org/published/workflow?id=4782a4943b6fa990
uniprot_rest_interface uniprot UniProt ID mapping and sequence retrieval 2015-10-09 https://github.com/jdrudolph/uniprot 0.6 requests To update Proteomics, Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 439 2162 2829 566 1035 2821 5928 56 56 902 902 0 0 0 0 980 3490 5885 21429 https://dev.workflowhub.eu/workflows/1026?version=1, https://dev.workflowhub.eu/workflows/1035?version=1, https://dev.workflowhub.eu/workflows/1143?version=2, https://dev.workflowhub.eu/workflows/1240?version=1, https://usegalaxy.eu/published/workflow?id=cde27d06b74ad2fd, https://usegalaxy.eu/published/workflow?id=d22dac11eba8c5a3, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c proteomics/maxquant-msstats-dda-lfq, proteomics/secretome-prediction
unique bg_uniq This tool returns all unique lines from a tab-separated file. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 551 625 6218 8855 0 0 0 0 0 0 0 0 49 49 392 392 600 1874 6610 22467 https://dev.workflowhub.eu/workflows/1035?version=1, https://dev.workflowhub.eu/workflows/1099?version=1, https://dev.workflowhub.eu/workflows/1116?version=1, https://dev.workflowhub.eu/workflows/1143?version=2, https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50, https://usegalaxy.eu/published/workflow?id=516b4d4146e4af66, https://usegalaxy.eu/published/workflow?id=6064d1dd87b458be, https://usegalaxy.eu/published/workflow?id=6f4bbed7a320dc2f, https://usegalaxy.eu/published/workflow?id=836cc09d17eaecb0, https://usegalaxy.eu/published/workflow?id=b46b51b2860b63d5, https://usegalaxy.eu/published/workflow?id=c9423228df977254, https://usegalaxy.eu/published/workflow?id=c94a1d028357c81e, https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960, https://usegalaxy.eu/published/workflow?id=cde27d06b74ad2fd, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=f7a7c72489d6b3d4, https://workflowhub.eu/workflows/117?version=1 assembly/metagenomics-assembly, ecology/ENA_Biodiv_submission, genome-annotation/bacterial-comparative-genomics-dataset-construction, microbiome/metagenomics-assembly, proteomics/secretome-prediction
varscan_version_2 varscan VarScan wrapper 2013-11-17 https://dkoboldt.github.io/varscan/ 2.4.2 varscan 2.4.6 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 631 763 7185 8578 2830 5950 16004 54780 420 484 2322 2741 44 44 152 152 3925 15091 25663 117577 https://usegalaxy.org/published/workflow?id=3771c5db96f8f246, https://usegalaxy.org/published/workflow?id=3d5347f1e8ee7db2, https://usegalaxy.org/published/workflow?id=683a0ab042fa34c9, https://usegalaxy.org/published/workflow?id=80b12b6e7ac8861f, https://usegalaxy.org/published/workflow?id=9a1b4c9747bf6ae0, https://usegalaxy.org/published/workflow?id=a37961bf3d435918, https://usegalaxy.org/published/workflow?id=a765dc267c6a5c3a, https://usegalaxy.org/published/workflow?id=a7a145c196aa55c9, https://usegalaxy.org/published/workflow?id=a7ee7de93a7fb261, https://usegalaxy.org/published/workflow?id=c4a1246974f279c5, https://usegalaxy.org/published/workflow?id=e2432c4d2b61705a, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86
vcf2pgsnp vcf2pgSnp VCF to pgSnp 2014-07-28 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 56 66 189 231 191 602 1331 2735 0 0 0 0 0 0 0 0 247 1162 1520 6006
vcf_annotate vcf_annotate Annotate a VCF file (dbSNP, hapmap) 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 1 28 54 220 340 0 0 0 0 28 112 220 782
vcf_extract vcf_extract Extract reads from a specified region 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 9 433 569 0 0 0 0 5 19 433 1435
vcf_filter vcf_filter Filter a VCF file 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 156 167 465 540 0 0 0 0 17 56 205 606 0 0 0 0 173 569 670 2486
vcf_intersect vcf_intersect Generate the intersection of two VCF files 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 19 0 0 0 0 18 28 287 463 0 0 0 0 18 67 287 1056
vcftools_annotate vcftools_annotate Annotate VCF using custom/user-defined annotations 2013-11-24 https://vcftools.github.io/ 0.1 echo To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 96 107 167 214 627 1368 1992 4211 12 16 128 156 2 2 2 2 737 2967 2289 9161 https://usegalaxy.org/published/workflow?id=a7a145c196aa55c9, https://usegalaxy.org/published/workflow?id=e7586d70715207b5, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86
vcftools_compare vcftools_compare Compare VCF files to get overlap and uniqueness statistics 2013-11-24 https://vcftools.github.io/ 0.1 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 132 157 465 637 0 0 0 0 0 12 0 16 0 0 0 0 132 433 465 1583
vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence 2016-10-16 https://vcftools.github.io/ 0.1.11 samtools 1.22 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
vcftools_isec vcftools_isec Intersect multiple VCF datasets 2013-11-24 https://vcftools.github.io/ 0.1.1 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 109 130 406 572 0 1 0 1 29 49 40 498 0 0 0 0 138 456 446 1963 https://usegalaxy.org.au/published/workflow?id=3d5deed70ac9bde4
vcftools_merge vcftools_merge Merge multiple VCF datasets into a single dataset 2013-11-24 https://vcftools.github.io/ 0.1.11 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 259 295 984 1283 0 0 0 0 45 63 93 455 0 0 0 0 304 966 1077 3892 https://usegalaxy.eu/published/workflow?id=c00fe92f9a579a15
vcftools_slice vcftools_slice Subset VCF dataset by genomic regions 2013-11-24 https://vcftools.github.io/ 0.1 echo To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 58 65 418 443 136 369 5343 8143 10 19 108 157 1 1 5 5 205 864 5874 20496
vcftools_subset vcftools_subset Select samples from a VCF dataset 2013-11-24 https://vcftools.github.io/ 0.1 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 45 50 125 144 0 0 0 0 11 19 104 142 0 0 0 0 56 181 229 744
venn_list venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.2.0 To update Graphics, Sequence Analysis, Visualization peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 700 831 4824 6098 968 2080 9871 18774 0 0 0 0 24 24 94 94 1692 6319 14789 54544 https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960
viennarna viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures 2015-02-28 http://www.tbi.univie.ac.at/RNA/ 2.2.10 viennarna 2.7.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 0 0 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 0 358 453 2895 8297 0 0 0 0 0 0 0 0 0 0 0 0 358 1169 2895 14087 https://usegalaxy.eu/published/workflow?id=58fd339165ded462, https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
vpt vpt_extract, vpt_segment Vizgen Post-processing Tool 2025-04-29 https://vizgen.github.io/vizgen-postprocessing/ 1.3.0 To update Single Cell, Spatial Omics, Transcriptomics, Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools/vpt https://github.com/bgruening/galaxytools/tree/master/tools/vpt 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
vrhyme vrhyme Tool for dereplication and binning virus genomes from metagenomes. 2025-05-14 https://github.com/AnantharamanLab/vRhyme 1.1.0 vrhyme 1.1.0 Up-to-date Metagenomics Scaffolding, Read binning, Read mapping, Sequence trimming Scaffolding, Read binning, Read mapping, Sequence trimming Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme vRhyme vRhyme vRhyme enables binning of viral genomes from metagenomes. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. 2015-02-28 0.2 vt 2015.11.10 To update Sequence Analysis, Variant Analysis bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval 2014-04-01 1.0.1 galaxy-ops 1.1.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 76 188 2308 0 0 0 0 0 0 0 0 17 110 188 2684
whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. 2024-04-23 https://github.com/bgruening/galaxytools/tree/master/tools/whisper 20231117 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisper https://github.com/bgruening/galaxytools/tree/master/tools/whisper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 234 234 0 0 0 0 0 0 0 0 0 0 0 0 18 54 234 702
windowsplitter winSplitter Make windows 2014-04-01 1.0.1 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 11 36 330 154 3963 0 0 0 0 0 0 0 0 36 404 154 4282
wordcloud wordcloud A little word cloud generator in Python. 2024-12-13 https://github.com/amueller/word_cloud 1.9.4 wordcloud To update Visualization bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 12 12 0 0 0 0 0 0 0 0 0 0 0 0 2 6 12 36 digital-humanities/text_mining_chinese
wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. 2018-06-12 https://github.com/ruanjue/wtdbg2 2.5 wtdbg 2.5 Up-to-date Assembly Genome assembly, De-novo assembly Genome assembly, De-novo assembly Sequence assembly, Sequencing Sequence assembly, Sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 369 416 1372 1826 0 0 0 0 0 0 0 0 26 26 142 142 395 1232 1514 4996
xy_plot XY_Plot_1 Plotting tool for multiple series and graph types 2013-09-25 1.0.2 r-base To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 771 928 4441 6254 2030 3933 6341 16255 564 612 2053 2341 99 99 340 340 3464 12500 13175 51540 https://dev.workflowhub.eu/workflows/1101?version=1, https://dev.workflowhub.eu/workflows/1129?version=1, https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.eu/published/workflow?id=25850714d13f0b0f, https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19, https://usegalaxy.eu/published/workflow?id=ce21961260fe4351, https://usegalaxy.eu/published/workflow?id=dadca1020f586338, https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8, https://usegalaxy.org.au/published/workflow?id=2717e90438c7fb8c, https://usegalaxy.org.au/published/workflow?id=5877e2d5eba79f36, https://usegalaxy.org/published/workflow?id=67080f040e855990, https://usegalaxy.org/published/workflow?id=6f090b2c259847d2, https://usegalaxy.org/published/workflow?id=746f4eef47648b26, https://usegalaxy.org/published/workflow?id=775335812a6b7a61, https://usegalaxy.org/published/workflow?id=9cc814d43379c2a6, https://usegalaxy.org/published/workflow?id=c50f10ecd1ac2ff9, https://usegalaxy.org/published/workflow?id=d653eaefcf6b4697, https://usegalaxy.org/published/workflow?id=e3c1736cca484dda, https://workflowhub.eu/workflows/652?version=1 microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short
AMRFinderPlus amrfinderplus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. 2023-05-12 https://github.com/ncbi/amr 3.12.8 ncbi-amrfinderplus 4.0.23 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus amrfinderplus AMRFinderPlus AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 533 533 10706 10706 316 316 7698 7698 0 0 0 0 16 16 774 774 865 2595 19178 57534 https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=7
Beacon2_Import beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. 2024-07-22 https://pypi.org/project/beacon2-import/ 2.2.4 beacon2-import 2.2.4 Up-to-date Variant Analysis Service discovery, Database search, Genetic variation analysis Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Genetic variation, Population genetics, Data security, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 51 51 0 0 0 0 0 0 0 0 0 0 0 0 10 30 51 153 variant-analysis/beacon_cnv_query, variant-analysis/beaconise_1000hg
ISEScan isescan "ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements." 2022-09-01 https://github.com/xiezhq/ISEScan 1.7.2.3 isescan 1.7.3 To update Sequence Analysis Structural variation detection Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation Genomics, Sequence analysis, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 274 274 63211 63211 106 106 435 435 90 90 5189 5189 29 29 909 909 499 1497 69744 209232 https://dev.workflowhub.eu/workflows/1136?version=2, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=9 genome-annotation/bacterial-genome-annotation
abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes 2016-07-29 https://github.com/tseemann/abricate 1.0.1 abricate 1.0.1 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Genomics, Microbiology Genomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 4981 5059 656194 672009 3701 3701 345048 345052 2259 2549 521371 537399 61 61 11594 11594 11002 33374 1534207 4634468 https://dev.workflowhub.eu/workflows/1091?version=1, https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=77e5bbd317750915, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f, https://usegalaxy.org.au/published/workflow?id=e20172eb0f30d6cd, https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=cce88bc57b180d09, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=7, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/470?version=1 microbiome/pathogen-detection-from-nanopore-foodborne-data
abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes 2023-04-03 https://zenodo.org/record/7370628 1.0.19 abritamr 1.0.19 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease, Antimicrobial resistance Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 194 194 1663 1663 0 0 0 0 0 0 0 0 0 0 0 0 194 582 1663 4989 https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://workflowhub.eu/workflows/634?version=1
abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler 2015-04-14 http://www.bcgsc.ca/platform/bioinfo/software/abyss 2.3.10 abyss 2.3.10 Up-to-date Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss abyss ABySS De novo genome sequence assembler using short reads. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 1090 1131 5811 6064 409 414 1286 1305 350 350 2224 2224 6 6 8 8 1855 5611 9329 28259
adapter_removal adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. 2022-05-04 https://github.com/MikkelSchubert/adapterremoval 2.3.4 adapterremoval 2.3.4 Up-to-date Fasta Manipulation, Sequence Analysis Sequence trimming, Sequence merging, Primer removal Sequence trimming, Sequence merging, Primer removal iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 71 71 517 517 0 0 0 0 0 0 0 0 0 0 0 0 71 213 517 1551
add_input_name_as_column addName Add input name as column on an existing tabular file 2020-03-24 https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column 0.2.0 python To update Text Manipulation mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 230 261 83660 93449 309 423 26182 27654 7 7 167 167 0 0 0 0 546 1783 110009 341288 https://dev.workflowhub.eu/workflows/1010?version=1, https://dev.workflowhub.eu/workflows/1314?version=2, https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=1f3f6757de60d3cf, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=389d992ff7268247, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc, https://usegalaxy.eu/published/workflow?id=89ed570bc0703472, https://usegalaxy.eu/published/workflow?id=9aa290ce1927d700, https://usegalaxy.eu/published/workflow?id=9e497c5c9e64d9b3, https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21, https://usegalaxy.eu/published/workflow?id=f4a55ef0d4c2cd97, https://usegalaxy.org.au/published/workflow?id=2fee25e188531691, https://usegalaxy.org.au/published/workflow?id=9016b2be61f89053, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org/published/workflow?id=450c2181f89e6b23, https://usegalaxy.org/published/workflow?id=f18e6fa5270fcd37, https://workflowhub.eu/workflows/1057?version=3 evolution/mtb_transmission
aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers 2021-01-03 https://github.com/BrendelGroup/AEGeAn 0.16.0 aegean 0.16.0 Up-to-date Transcriptomics, Sequence Analysis Sequence annotation Sequence annotation Sequence analysis, Gene structure Sequence analysis, Gene structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean gaeval GAEVAL Gene Annotation EVAluation. 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 99 99 256 256 47 47 103 103 56 56 2211 2211 27 27 49 49 229 687 2619 7857 https://dev.workflowhub.eu/workflows/1202?version=1, https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://workflowhub.eu/workflows/754?version=1 genome-annotation/funannotate
aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account 2022-06-29 https://github.com/ggloor/ALDEx_bioc 1.26.0 bioconductor-aldex2 1.38.0 To update Metagenomics Statistical inference Statistical inference Gene expression, Statistics and probability Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 47 299 299 0 0 0 0 0 0 0 0 0 0 0 0 47 141 299 897
allegro allegro Linkage and haplotype analysis from deCODE 2017-11-19 http://www.decode.com/software/ 2 allegro 3 To update Variant Analysis Sequence motif discovery Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA Sequence analysis, Transcription factors and regulatory sites, DNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
amplican amplican AmpliCan is an analysis tool for genome editing. 2021-09-22 https://github.com/valenlab/amplican 1.14.0 bioconductor-amplican 1.28.0 To update Sequence Analysis Alignment, Standardisation and normalisation Alignment, Standardisation and normalisation PCR experiment, Statistics and probability PCR experiment, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 84 84 0 0 0 0 0 0 0 0 0 0 0 0 18 54 84 252
ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_export_otu, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 2022-04-04 https://github.com/MadsAlbertsen/ampvis2/ 2.8.9 To update Metagenomics Analysis, Visualisation Analysis, Visualisation Biodiversity Biodiversity iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. 1 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 205 205 2708 2708 4 4 4 4 0 0 0 0 0 0 0 0 209 627 2712 8136 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=478c921b4914169c, https://workflowhub.eu/workflows/1275?version=1
ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. 2022-07-16 https://github.com/FrederickHuangLin/ANCOMBC 1.4.0 bioconductor-ancombc 2.8.0 To update Metagenomics DNA barcoding DNA barcoding Microbial ecology, Metagenomics, Taxonomy Microbial ecology, Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 37 37 0 0 0 0 0 0 0 0 0 0 0 0 9 27 37 111
anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects 2019-03-21 https://anndata.readthedocs.io 0.10.9 anndata 0.6.22.post1 To update Single Cell, Spatial Omics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata anndata anndata From https://anndata.readthedocs.io/en/latest/"Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray." 5 5 5 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 2041 2070 46937 47633 994 994 19201 19201 316 316 10481 10481 0 0 0 0 3351 10082 76619 230553 https://dev.workflowhub.eu/workflows/1012?version=1, https://dev.workflowhub.eu/workflows/1013?version=1, https://dev.workflowhub.eu/workflows/1014?version=1, https://dev.workflowhub.eu/workflows/1015?version=1, 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https://workflowhub.eu/workflows/468?version=3, https://workflowhub.eu/workflows/512?version=2, https://workflowhub.eu/workflows/513?version=3, https://workflowhub.eu/workflows/646?version=2 single-cell/bulk-music-2-preparescref, single-cell/pseudobulk-analysis, single-cell/scatac-batch-correction-snapatac2, single-cell/scatac-preprocessing-tenx, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_alevin, single-cell/scrna-case_alevin-combine-datasets, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_cell-cycle, single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-case_trajectories, single-cell/scrna-data-ingest, single-cell/scrna-ncbi-anndata, single-cell/scrna-plant, single-cell/scrna-scanpy-pbmc3k
anndata2ri anndata2ri Convert between Anndata and SingCellExperiment objects 2025-02-12 https://github.com/theislab/anndata2ri 1.3.2 anndata2ri 1.3.2 Up-to-date Single Cell, Convert Formats Data handling Data handling iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata2ri/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata2ri anndata2ri anndata2ri RPy2 converter from AnnData to SingleCellExperiment and back. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages 2017-11-17 https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.20.0 To update Genome annotation Annotation Annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 3232 3439 31518 34272 6524 7241 60687 72517 1138 1160 6237 6380 22 22 148 148 10916 33694 98590 310497 https://dev.workflowhub.eu/workflows/1230?version=1, https://dev.workflowhub.eu/workflows/1261?version=1, https://dev.workflowhub.eu/workflows/1321?version=1, https://dev.workflowhub.eu/workflows/1332?version=1, https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=0f7acf235096b708, https://usegalaxy.eu/published/workflow?id=227d97974573aaf2, https://usegalaxy.eu/published/workflow?id=2ae4a83327615155, https://usegalaxy.eu/published/workflow?id=2f7c04ad219a9d2d, https://usegalaxy.eu/published/workflow?id=3386856a60b35897, https://usegalaxy.eu/published/workflow?id=33f23578677b384d, https://usegalaxy.eu/published/workflow?id=36eefcc25ab1fe15, https://usegalaxy.eu/published/workflow?id=6d47a24218d08930, https://usegalaxy.eu/published/workflow?id=a6290cdfa12d34ad, https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960, https://usegalaxy.eu/published/workflow?id=f98f0e0c18222cc0, https://usegalaxy.eu/published/workflow?id=f9ddc4dd9140b293, https://usegalaxy.eu/published/workflow?id=fe6c64676be56ee9, https://usegalaxy.org.au/published/workflow?id=bdb498b1f0e8944f, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://workflowhub.eu/workflows/689?version=1 single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music-2-preparescref, single-cell/bulk-music-3-preparebulk, transcriptomics/minerva-pathways, transcriptomics/rna-seq-counts-to-genes
argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database 2024-08-28 https://github.com/BigDataBiology/argNorm 1.0.0 argnorm 1.0.0 Up-to-date Genome annotation Gene functional annotation Gene functional annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 49 49 0 0 0 0 0 0 0 0 1 1 27 27 22 66 76 228
arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR 2022-07-27 https://github.com/suhrig/arriba 2.5.0 arriba 2.5.0 Up-to-date Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 93 93 3866 3866 14 14 112 112 16 16 338 338 0 0 0 0 123 369 4316 12948 https://dev.workflowhub.eu/workflows/1383?version=1, https://usegalaxy.org.au/published/workflow?id=0dff588f31f1dfd6, https://usegalaxy.org.au/published/workflow?id=65250d6b30d4bc7c, https://usegalaxy.org.au/published/workflow?id=d5a3fd1faa3f0a41, https://usegalaxy.org/published/workflow?id=39810594e5c332d5, https://usegalaxy.org/published/workflow?id=b28789b6a0e1f5c9 proteomics/neoantigen-1-fusion-database-generation
art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data 2015-02-11 http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ 2014.11.03.0 art 2016.06.05 To update Sequence Analysis, Data Source Conversion Conversion Bioinformatics Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 259 259 0 0 0 0 0 0 0 0 0 0 0 0 21 63 259 777
artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building 2020-04-17 https://github.com/artic-network/fieldbioinformatics 1.6.0 artic 1.7.1 To update Sequence Analysis Sequence alignment Sequence alignment Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 271 271 11912 11912 0 0 0 0 12 12 531 531 0 0 0 0 283 849 12443 37329 https://workflowhub.eu/workflows/521?version=1
assembly_stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. 2023-06-21 https://github.com/rjchallis/assembly-stats 17.02 rjchallis-assembly-stats 17.02 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 26 26 14 42 26 78
astral astral Tool for estimating an unrooted species tree given a set of unrooted gene trees 2024-08-28 https://github.com/smirarab/ASTRAL 5.7.8 astral-tree 5.7.8 Up-to-date Phylogenetics iuc https://github.com/usegalaxy-be/galaxytools/tree/main/astral https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 5 5 151 151 0 0 0 0 5 15 151 453 https://workflowhub.eu/workflows/359?version=1
augustus augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. 2017-10-05 http://bioinf.uni-greifswald.de/augustus/ 3.4.0 augustus 3.5.0 To update Sequence Analysis Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families Gene transcripts, Gene and protein families bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 2091 2342 14780 16318 3002 3002 17131 17131 569 569 7735 7735 51 51 4656 4656 5713 17390 44302 134444 https://dev.workflowhub.eu/workflows/1164?version=2, https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1 genome-annotation/annotation-with-maker
autobigs autobigs-cli Automated MLST typing from PubMLST and InstitutPasteur. 2025-02-24 https://github.com/Syph-and-VPD-Lab/autoBIGS.cli 0.6.2 autobigs-cli 0.6.5 To update Sequence Analysis iuc https://github.com/Syph-and-VPD-Lab/autoBIGS.cli https://github.com/galaxyproject/tools-iuc/tree/main/tools/autobigs AutoBIGS.CLI AutoBIGS.CLI A command-line interface (CLI) based program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV. Capable of querying a variety of MLST databases from both Institut Pasteur and PubMLST. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. 2022-08-09 https://bio2byte.be 3.0.5+galaxy0 b2btools 3.0.7 To update Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology Protein disorder prediction, Protein secondary structure prediction, Protein feature detection Protein disorder prediction, Protein secondary structure prediction iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 20 20 372 372 0 0 0 0 0 0 0 0 0 0 0 0 20 60 372 1116
bakta bakta "Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." 2022-09-01 https://github.com/oschwengers/bakta 1.9.4 bakta 1.11.0 To update Sequence Analysis Genome annotation Genome annotation Genomics, Sequence analysis, Bioinformatics Genomics, Sequence analysis, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 901 901 16861 16861 333 333 2041 2041 238 238 18219 18219 56 56 1931 1931 1528 4584 39052 117156 https://dev.workflowhub.eu/workflows/1136?version=2, https://dev.workflowhub.eu/workflows/1168?version=2, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=9 genome-annotation/amr-gene-detection, genome-annotation/bacterial-genome-annotation
bam2fastx bam2fastx Convert PacBio Bam File to fasta or fastq file 2024-03-11 https://github.com/PacificBiosciences/pbtk 3.5.0 pbtk 3.5.0 Up-to-date Convert Formats, Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 34 126 126 38 38 277 277 0 0 0 0 0 0 0 0 72 216 403 1209
bam_to_scidx bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. 2015-12-07 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx 1.0.1 openjdk To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13 20 57 131 42 210 286 788 0 0 0 0 0 0 0 0 55 340 343 1605
bamtools bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.3 To update Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 4 3 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 488 488 20731 20731 338 338 4702 4702 23 23 227 227 0 0 0 0 849 2547 25660 76980 https://dev.workflowhub.eu/workflows/1087?version=2, https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c, https://usegalaxy.eu/published/workflow?id=bc5ced57e711acf9, https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b, https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2, https://usegalaxy.org/published/workflow?id=574e42683dc3961b, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1260?version=1 microbiome/pathogen-detection-from-nanopore-foodborne-data, variant-analysis/aiv-analysis
bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.3 To update Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 624 734 14256 15720 1477 5710 60638 101980 4 4 120 120 13 13 54 54 2118 10697 75068 268010 https://dev.workflowhub.eu/workflows/1099?version=1, https://dev.workflowhub.eu/workflows/1116?version=1, https://usegalaxy.eu/published/workflow?id=36a4646959829018, https://usegalaxy.eu/published/workflow?id=99022559adf01c4a, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1 assembly/metagenomics-assembly, microbiome/metagenomics-assembly
bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.3 To update Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3327 3618 121087 131737 6716 11234 98496 150535 555 555 6901 6901 470 471 2129 2192 11068 38014 228613 748591 https://dev.workflowhub.eu/workflows/1081?version=1, https://dev.workflowhub.eu/workflows/1100?version=2, 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bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. 2021-03-29 https://github.com/statgen/bamUtil bamutil 1.0.15 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 47 47 23 23 71 71 1 1 318 318 0 0 0 0 45 135 436 1308
bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily 2018-09-06 https://github.com/rrwick/Bandage 2022.09 bandage_ng 2025.6.1 To update Visualization Sequence assembly visualisation Sequence assembly visualisation Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 2 2 2 0 5663 5844 63829 65480 6120 6120 57281 57281 3498 3498 21301 21301 339 339 7771 7771 15620 47041 150182 452197 https://dev.workflowhub.eu/workflows/1005?version=1, https://dev.workflowhub.eu/workflows/1091?version=1, https://dev.workflowhub.eu/workflows/1103?version=1, https://dev.workflowhub.eu/workflows/1107?version=1, https://dev.workflowhub.eu/workflows/1120?version=1, https://dev.workflowhub.eu/workflows/1127?version=3, https://dev.workflowhub.eu/workflows/1132?version=2, https://dev.workflowhub.eu/workflows/1135?version=2, https://dev.workflowhub.eu/workflows/1139?version=1, https://dev.workflowhub.eu/workflows/1170?version=2, https://dev.workflowhub.eu/workflows/1178?version=1, https://dev.workflowhub.eu/workflows/1197?version=2, https://dev.workflowhub.eu/workflows/39?version=1, https://dev.workflowhub.eu/workflows/584?version=1, 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barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes 2019-02-21 https://bitbucket.org/princeton_genomics/barcode_splitter/ 0.18.4.0 barcode_splitter 0.18.6 To update Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. 2023-09-06 https://github.com/lldelisle/baredSC 1.1.3 baredsc 1.1.3 Up-to-date Single Cell, Transcriptomics, Visualization Data retrieval, Expression correlation analysis, Differential gene expression profiling Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 11 11 114 114 13 13 33 33 4 4 168 168 0 0 0 0 28 84 315 945 https://usegalaxy.eu/published/workflow?id=2da3c41ad5c11c3b, https://usegalaxy.eu/published/workflow?id=3410a75a2a4899dc, https://usegalaxy.eu/published/workflow?id=4025b5dca188e6a4, https://usegalaxy.eu/published/workflow?id=49d913cefc5daaf3, https://usegalaxy.eu/published/workflow?id=4eb8aec8a5be98b3, https://usegalaxy.eu/published/workflow?id=72c03f7b5bc9fb9d, https://usegalaxy.eu/published/workflow?id=7341ca7572447d60, https://usegalaxy.eu/published/workflow?id=967f890c0883f72a, https://usegalaxy.eu/published/workflow?id=cdf782de6c67477a, https://usegalaxy.eu/published/workflow?id=da41880826c3d758, https://usegalaxy.org.au/published/workflow?id=2436bc493e76f438, https://usegalaxy.org.au/published/workflow?id=31a664d151978dc6, https://usegalaxy.org.au/published/workflow?id=481c666fbc7ffa02, https://usegalaxy.org.au/published/workflow?id=51aaafbd00b91717, https://usegalaxy.org.au/published/workflow?id=579da54989f5d55c, https://usegalaxy.org.au/published/workflow?id=5e3ff382ab802baf, https://usegalaxy.org.au/published/workflow?id=ac4799c5009f98d3, https://usegalaxy.org.au/published/workflow?id=b73280eaeb77a0a9, https://usegalaxy.org.au/published/workflow?id=d01ff75a4943fa79, https://usegalaxy.org.au/published/workflow?id=d6521e6c247eeaaf, https://usegalaxy.org/published/workflow?id=0f6bb7847f8769af, https://usegalaxy.org/published/workflow?id=1a08efa0bf83d225, https://usegalaxy.org/published/workflow?id=3d0f92e7f63978b6, https://usegalaxy.org/published/workflow?id=6cad14c78ec330ac, https://usegalaxy.org/published/workflow?id=6f1da4e0830e6051, https://usegalaxy.org/published/workflow?id=84112c29ee53a5db, https://usegalaxy.org/published/workflow?id=92b67534076ae889, https://usegalaxy.org/published/workflow?id=e3366346808b1f55, https://usegalaxy.org/published/workflow?id=ebdf324634e7243c, https://usegalaxy.org/published/workflow?id=fd511165e30cb62c, https://usegalaxy.org/published/workflow?id=ff84d87fd3638a3f, https://workflowhub.eu/workflows/615?version=5
barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. 2017-08-25 https://github.com/tseemann/barrnap 1.2.2 barrnap 0.9 To update Sequence Analysis Gene prediction Gene prediction Genomics, Model organisms, Model organisms Genomics, Model organisms, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 414 414 7731 7731 0 0 0 0 240 350 7118 8132 17 17 235 235 671 2123 15084 46266 https://usegalaxy.eu/published/workflow?id=e8eb80ee09159bac
basil basil Breakpoint detection, including large insertions 2019-05-22 https://github.com/seqan/anise_basil 1.2.0 anise_basil 1.2.0 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79 84 280 317 109 109 487 489 0 0 0 0 0 0 0 0 188 569 767 2340 https://usegalaxy.org/published/workflow?id=e67b6da41e1e6932
bax2bam bax2bam BAX to BAM converter 2019-10-12 https://github.com/pacificbiosciences/bax2bam/ 0.0.11 bax2bam 0.0.11 Up-to-date Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20 26 154 208 32 32 212 212 0 0 0 0 0 0 0 0 52 162 366 1152
bayescan BayeScan Detecting natural selection from population-based genetic data 2017-03-09 http://cmpg.unibe.ch/software/BayeScan/index.html 2.1 bayescan 2.0.1 To update Sequence Analysis Statistical inference Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 32 104 104 0 0 0 0 0 0 0 0 0 0 0 0 32 96 104 312
bbgbigwig bbgtobigwig Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. 2024-06-14 https://www.encodeproject.org/software/bedgraphtobigwig/ 0.1 ucsc-bedgraphtobigwig 481 To update Convert Formats Sequence analysis Sequence analysis iuc https://www.encodeproject.org/software/bedgraphtobigwig/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 23 219 219 121 121 863 863 0 0 0 0 0 0 0 0 144 432 1082 3246 https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=e522be58f0bac656 epigenetics/formation_of_super-structures_on_xi
bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. 2021-10-04 https://jgi.doe.gov/data-and-tools/bbtools/ 39.08 bbmap 39.26 To update Sequence Analysis RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools bbmap BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. 6 3 6 6 0 0 0 0 0 0 0 0 0 0 0 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 906 906 16089 16089 924 924 6953 6953 134 134 2968 2968 0 0 0 0 1964 5892 26010 78030 https://usegalaxy.org.au/published/workflow?id=25f65a29ce3c3ee0, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/519?version=1
bcftools bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers 2015-08-12 https://samtools.github.io/bcftools/ 1.15.1 bcftools 1.22 To update Variant Analysis Data handling, Variant calling Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment DNA polymorphism, GWAS study, Genotyping experiment iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 2017-10-05 https://github.com/dmaticzka/bctools 0.2.2 bctools 0.2.2 Up-to-date Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 241 282 1978 3130 0 0 0 0 0 0 0 0 0 0 0 0 241 764 1978 7086 https://dev.workflowhub.eu/workflows/1285?version=2, https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c transcriptomics/clipseq
beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). 2023-08-11 https://github.com/EGA-archive/beacon2-ri-tools/tree/main 2.0.0 beacon2-ri-tools 2.0.0 Up-to-date Variant Analysis Service discovery, Database search, Genetic variation analysis Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Genetic variation, Population genetics, Data security, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 15 15 52 52 0 0 0 0 0 0 0 0 0 0 0 0 15 45 52 156
beagle beagle Beagle is a program for phasing and imputing missing genotypes. 2021-07-03 https://faculty.washington.edu/browning/beagle/beagle.html 5.4_29Oct24.c8e beagle 5.4_22Jul22.46e To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 32 32 137 137 0 0 0 0 0 0 0 0 0 0 0 0 32 96 137 411
bedops_sortbed bedops-sort-bed BEDOPS: high-performance genomic feature operations 2023-08-08 https://bedops.readthedocs.io/en/latest/ 2.4.42 bedops 2.4.42 Up-to-date Genomic Interval Operations iuc https://bedops.readthedocs.io/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 62 62 184 184 85 85 273 273 0 0 0 0 0 0 0 0 147 441 457 1371
bedtools bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic 2014-09-13 https://github.com/arq5x/bedtools2 2.31.1 bedtools 2.31.1 Up-to-date Genomic Interval Operations, Text Manipulation Mapping Mapping Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. 37 37 37 37 0 0 0 0 0 0 0 0 0 0 0 37 6 37 0 0 0 0 0 0 37 0 0 0 0 0 37 37 37 0 14657 16452 943491 1002560 26553 44252 405712 674852 2756 3158 87815 96143 942 966 8935 9359 44908 154644 1445953 4674820 https://dev.workflowhub.eu/workflows/1002?version=1, https://dev.workflowhub.eu/workflows/1012?version=1, https://dev.workflowhub.eu/workflows/1077?version=2, https://dev.workflowhub.eu/workflows/1106?version=2, https://dev.workflowhub.eu/workflows/1113?version=2, https://dev.workflowhub.eu/workflows/1153?version=2, https://dev.workflowhub.eu/workflows/1161?version=1, https://dev.workflowhub.eu/workflows/1169?version=2, https://dev.workflowhub.eu/workflows/1175?version=2, https://dev.workflowhub.eu/workflows/1187?version=2, 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https://workflowhub.eu/workflows/138?version=5, https://workflowhub.eu/workflows/356?version=1, https://workflowhub.eu/workflows/395?version=15, https://workflowhub.eu/workflows/399?version=19, https://workflowhub.eu/workflows/400?version=12, https://workflowhub.eu/workflows/401?version=13, https://workflowhub.eu/workflows/561?version=11, https://workflowhub.eu/workflows/625?version=13, https://workflowhub.eu/workflows/878?version=1 assembly/ecoli_comparison, assembly/vgp_genome_assembly, epigenetics/atac-seq, epigenetics/cut_and_run, epigenetics/formation_of_super-structures_on_xi, epigenetics/tal1-binding-site-identification, genome-annotation/repeatmasker, introduction/galaxy-intro-101, microbiome/pathogen-detection-from-nanopore-foodborne-data, single-cell/scatac-preprocessing-tenx, transcriptomics/clipseq
bellavista bellavista_prepare Open-Source Visualization for Imaging-Based Spatial Transcriptomics 2025-05-02 https://github.com/pkosurilab/BellaVista 0.0.2 To update Single Cell, Spatial Omics, Transcriptomics, Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bellavista https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellavista 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bellerophon bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. 2021-05-28 https://github.com/davebx/bellerophon 1.0 bellerophon 1.0 Up-to-date Sequence Analysis iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 293 293 1850 1850 86 86 1278 1278 31 31 671 671 0 0 0 0 410 1230 3799 11397 https://dev.workflowhub.eu/workflows/1002?version=1, https://dev.workflowhub.eu/workflows/1127?version=3, https://dev.workflowhub.eu/workflows/1187?version=2, https://usegalaxy.eu/published/workflow?id=069d99391a69baf4, https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920, https://usegalaxy.eu/published/workflow?id=3010ecad1a342331, https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f, https://usegalaxy.eu/published/workflow?id=3b57fc81001667b5, https://usegalaxy.eu/published/workflow?id=4949751217c0e211, https://usegalaxy.eu/published/workflow?id=652433160b04b232, https://usegalaxy.eu/published/workflow?id=792b24fc23bd3071, https://usegalaxy.eu/published/workflow?id=a37d1e0db16cfb67, https://usegalaxy.eu/published/workflow?id=a53f78aa6866b811, https://usegalaxy.eu/published/workflow?id=b287bb779cf686ef, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=bc8ccd13a07bd9ec, https://usegalaxy.eu/published/workflow?id=c8f94a2e838fc0f1, https://usegalaxy.eu/published/workflow?id=feeb1fa358ccf328, https://usegalaxy.org.au/published/workflow?id=0aa316f8c6cff444, https://usegalaxy.org.au/published/workflow?id=0dbb85f727302a72, https://usegalaxy.org.au/published/workflow?id=29f0c07c8a24b542, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=455e68f185fec41b, https://usegalaxy.org.au/published/workflow?id=6c1c11a81a2ab1b8, https://usegalaxy.org.au/published/workflow?id=6ec5728eec9c26d7, https://usegalaxy.org.au/published/workflow?id=7028436ef03171cc, https://usegalaxy.org.au/published/workflow?id=77b2fcf8c805ad5d, https://usegalaxy.org.au/published/workflow?id=7a97e8ccc332c1e8, https://usegalaxy.org.au/published/workflow?id=86eb0ea9dc230f04, https://usegalaxy.org.au/published/workflow?id=ae6a03240680712a, https://usegalaxy.org.au/published/workflow?id=b9e89401313a0cca, https://usegalaxy.org.au/published/workflow?id=be35847680078c90, https://usegalaxy.org.au/published/workflow?id=cac0b8a09d59044b, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467, https://usegalaxy.org.au/published/workflow?id=fdec6e2fcd5e2cf5, https://usegalaxy.org/published/workflow?id=155839aeb6340f54, https://usegalaxy.org/published/workflow?id=28dbbfb3d480f4b1, https://usegalaxy.org/published/workflow?id=28ddea356ae57da1, https://usegalaxy.org/published/workflow?id=3d805d7e0f34c727, https://usegalaxy.org/published/workflow?id=3db51822f04f4ff7, https://usegalaxy.org/published/workflow?id=6341c384ceaf47ed, https://usegalaxy.org/published/workflow?id=88327cb2e0fe3c25, https://usegalaxy.org/published/workflow?id=903e35b62946ed76, https://usegalaxy.org/published/workflow?id=9f4c4038d1c519e2, https://usegalaxy.org/published/workflow?id=a4a6d6846c1692f9, https://usegalaxy.org/published/workflow?id=afa89bb0e8966753, https://workflowhub.eu/workflows/1054?version=1, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/625?version=13, https://workflowhub.eu/workflows/702?version=1 assembly/ERGA-post-assembly-QC, assembly/vgp_genome_assembly
berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. 2019-03-08 https://github.com/tseemann/berokka 0.2.3 berokka 0.2.3 Up-to-date Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 73 73 1024 1024 0 0 0 0 73 219 1024 3072
bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF 2024-02-18 https://github.com/medema-group/BiG-SCAPE 1.1.9 bigscape 1.1.9 Up-to-date Metagenomics Clustering, Global alignment, Fold recognition Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 43 1196 1196 0 0 0 0 0 0 0 0 0 0 0 0 43 129 1196 3588
bigwig_outlier_bed bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files 2024-07-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed 0.2.4 python To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed bigtools bigtools Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11 877 877 21 21 687 687 0 0 0 0 0 0 0 0 32 96 1564 4692 https://usegalaxy.eu/published/workflow?id=3b94f511c52da835
binette binette Binning refinement tool 2025-01-14 https://github.com/genotoul-bioinfo/Binette 1.1.1 binette 1.1.1 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binette/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette binette Binette Binette is a fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://usegalaxy.eu/published/workflow?id=b0377f05f97b18b1
binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. 2022-02-18 https://github.com/songweizhi/Binning_refiner 1.4.3 binning_refiner 1.4.3 Up-to-date Metagenomics Read binning, Sequence clustering Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Metagenomics, Sequence assembly, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 50 50 161 161 0 0 0 0 0 0 0 0 0 0 0 0 50 150 161 483
bio_hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation 2017-09-29 https://github.com/phac-nml/bio_hansel 2.6.1 bio_hansel 2.6.1 Up-to-date Sequence Analysis Genotyping, SNP detection, Genome assembly Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 33 332 360 58 58 377 377 0 0 0 0 0 0 0 0 90 271 709 2155
bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! 2016-11-03 https://pypi.python.org/pypi/biopython-extensions/ 0.21.9 python-bioext 0.21.9 Up-to-date Next Gen Mappers iuc https://github.com/davebx/bioext-gx/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 987 987 31488 31488 2316 2316 18020 18020 1 1 2 2 0 0 0 0 3304 9912 49510 148530 https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org/published/workflow?id=4884918895db9af0, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=c03c18813a3380b3
bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics 2023-01-25 https://github.com/dariober/bioinformatics-cafe/ 0.1.0 python To update Sequence Analysis mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 110 110 1524 1524 95 95 1168 1168 0 0 0 0 0 0 0 0 205 615 2692 8076 https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=629e57958afed44c variant-analysis/pox-tiled-amplicon, variant-analysis/sars-cov-2-variant-discovery
biomformat biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. 2016-06-07 https://github.com/biocore/biom-format 2.1.15 biom-format 2.1.7 To update Metagenomics Formatting Formatting Laboratory information management, Sequence analysis Laboratory information management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format biomformat biomformat This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. 2 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 351 351 14928 14928 449 676 2771 5214 210 250 2268 2569 0 0 0 0 1010 3297 19967 62645 https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977, https://usegalaxy.eu/published/workflow?id=169327ba670607d1, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=20d472fc5563a640, https://usegalaxy.org.au/published/workflow?id=4f837b7f90d5ebac, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://usegalaxy.org.au/published/workflow?id=ca6f29110df8dadc, https://workflowhub.eu/workflows/1270?version=1, https://workflowhub.eu/workflows/1273?version=1, https://workflowhub.eu/workflows/142?version=1, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1
biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. 2020-01-17 https://www.sanger.ac.uk/science/tools/bio-tradis 1.4.5 biotradis 1.4.5 Up-to-date Genome annotation Sequence analysis Sequence analysis Mobile genetic elements, Workflows Mobile genetic elements, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 421 421 6465 6465 0 0 0 0 0 0 0 0 421 1263 6465 19395
biscot biscot Bionano scaffolding correction tool 2023-01-06 https://github.com/institut-de-genomique/biscot 2.3.3 biscot 2.3.3 Up-to-date Assembly iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 3 3 0 0 0 0 0 0 0 0 0 0 0 0 1 3 3 9
blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 2015-05-25 https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 To update Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 112 114 770 784 69 69 181 181 18 18 157 157 0 0 0 0 199 599 1108 3338 https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6
bowtie2 bowtie2 Bowtie2: Fast and sensitive read alignment 2017-05-08 http://bowtie-bio.sourceforge.net/bowtie2 2.5.3 bowtie2 2.5.4 To update Next Gen Mappers Read mapping Read mapping Mapping, Genomics, Mapping Mapping, Genomics, Mapping devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. 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bp_genbank2gff3 bp_genbank2gff3 Converts GenBank format files to GFF3 2015-08-14 https://bioperl.org/ 1.1 perl-bioperl 1.7.8 To update Sequence Analysis Data handling, Service invocation Data handling, Service invocation Genomics, Software engineering, Data management Genomics, Software engineering iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 536 581 7942 8735 928 928 10508 10512 170 178 8949 8990 18 18 223 223 1652 5009 27622 83704 genome-annotation/secondary-metabolite-discovery
bracken est_abundance Bayesian Reestimation of Abundance with KrakEN 2019-10-15 https://github.com/jenniferlu717/Bracken/releases 3.1 bracken 3.1 Up-to-date Sequence Analysis, Metagenomics Statistical calculation Statistical calculation Metagenomics, Microbial ecology Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1070 1070 79390 79390 416 416 17034 17034 137 137 3009 3009 32 32 4896 4896 1655 4965 104329 312987 https://dev.workflowhub.eu/workflows/1095?version=1, https://dev.workflowhub.eu/workflows/1217?version=2, https://dev.workflowhub.eu/workflows/1344?version=1, https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502, https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88, https://usegalaxy.eu/published/workflow?id=0c47571d20535426, https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=47e14222073e7192, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=884a4415b669690c, https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=ebb131f2a6172081, https://usegalaxy.fr/published/workflow?id=3d3b40398d1cd1ae, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, https://usegalaxy.org/published/workflow?id=1be5c982c2d36a6c, https://usegalaxy.org/published/workflow?id=623fc80c7f91a33a, https://usegalaxy.org/published/workflow?id=9f68718f025bed30, https://usegalaxy.org/published/workflow?id=b6a795834009ce06, https://workflowhub.eu/workflows/1052?version=8, https://workflowhub.eu/workflows/1199?version=2 ecology/bacterial-isolate-species-contamination-checking, microbiome/taxonomic-profiling, sequence-analysis/quality-contamination-control
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bwa_mem2 bwa_mem2_idx, bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. 2021-10-08 https://github.com/bwa-mem2/bwa-mem2 2.2.1 bwa-mem2 2.2.1 Up-to-date Next Gen Mappers Sequence alignment Sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 0 2937 2937 72774 72774 3583 3583 54684 54684 866 866 24846 24846 42 42 385 385 7428 22284 152689 458067 https://dev.workflowhub.eu/workflows/1002?version=1, https://dev.workflowhub.eu/workflows/1127?version=3, https://dev.workflowhub.eu/workflows/1178?version=1, https://dev.workflowhub.eu/workflows/1187?version=2, https://usegalaxy.eu/published/workflow?id=069d99391a69baf4, https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=22454322d370b3ff, https://usegalaxy.eu/published/workflow?id=3010ecad1a342331, https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f, https://usegalaxy.eu/published/workflow?id=3b57fc81001667b5, https://usegalaxy.eu/published/workflow?id=4949751217c0e211, https://usegalaxy.eu/published/workflow?id=54a4f76a5d736011, https://usegalaxy.eu/published/workflow?id=652433160b04b232, https://usegalaxy.eu/published/workflow?id=792b24fc23bd3071, https://usegalaxy.eu/published/workflow?id=8edf456f4aeddaac, https://usegalaxy.eu/published/workflow?id=a37d1e0db16cfb67, https://usegalaxy.eu/published/workflow?id=a53f78aa6866b811, https://usegalaxy.eu/published/workflow?id=a99303884d7e5fe2, https://usegalaxy.eu/published/workflow?id=b287bb779cf686ef, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=bc8ccd13a07bd9ec, https://usegalaxy.eu/published/workflow?id=c8f94a2e838fc0f1, https://usegalaxy.eu/published/workflow?id=feeb1fa358ccf328, https://usegalaxy.org.au/published/workflow?id=0aa316f8c6cff444, https://usegalaxy.org.au/published/workflow?id=0dbb85f727302a72, https://usegalaxy.org.au/published/workflow?id=29f0c07c8a24b542, https://usegalaxy.org.au/published/workflow?id=44bad90b676d58f6, https://usegalaxy.org.au/published/workflow?id=455e68f185fec41b, https://usegalaxy.org.au/published/workflow?id=49b5c35b9723fa62, https://usegalaxy.org.au/published/workflow?id=6c1c11a81a2ab1b8, https://usegalaxy.org.au/published/workflow?id=6ec5728eec9c26d7, https://usegalaxy.org.au/published/workflow?id=7028436ef03171cc, https://usegalaxy.org.au/published/workflow?id=77b2fcf8c805ad5d, https://usegalaxy.org.au/published/workflow?id=7a97e8ccc332c1e8, https://usegalaxy.org.au/published/workflow?id=86eb0ea9dc230f04, https://usegalaxy.org.au/published/workflow?id=ae6a03240680712a, https://usegalaxy.org.au/published/workflow?id=b9e89401313a0cca, https://usegalaxy.org.au/published/workflow?id=be35847680078c90, https://usegalaxy.org.au/published/workflow?id=cac0b8a09d59044b, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467, https://usegalaxy.org.au/published/workflow?id=f7adc76331620f34, https://usegalaxy.org.au/published/workflow?id=fdec6e2fcd5e2cf5, https://usegalaxy.org/published/workflow?id=155839aeb6340f54, https://usegalaxy.org/published/workflow?id=28dbbfb3d480f4b1, https://usegalaxy.org/published/workflow?id=28ddea356ae57da1, https://usegalaxy.org/published/workflow?id=3d805d7e0f34c727, https://usegalaxy.org/published/workflow?id=3db51822f04f4ff7, https://usegalaxy.org/published/workflow?id=5951d11d3122abed, https://usegalaxy.org/published/workflow?id=6341c384ceaf47ed, https://usegalaxy.org/published/workflow?id=6d68f56abf9c624d, https://usegalaxy.org/published/workflow?id=88327cb2e0fe3c25, https://usegalaxy.org/published/workflow?id=903e35b62946ed76, https://usegalaxy.org/published/workflow?id=9f4c4038d1c519e2, https://usegalaxy.org/published/workflow?id=a4a6d6846c1692f9, https://usegalaxy.org/published/workflow?id=afa89bb0e8966753, https://workflowhub.eu/workflows/1054?version=1, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/347?version=1, https://workflowhub.eu/workflows/351?version=1, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/625?version=13, https://workflowhub.eu/workflows/702?version=1, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1 assembly/ERGA-post-assembly-QC, assembly/mrsa-nanopore, assembly/vgp_genome_assembly, introduction/galaxy-intro-ngs-data-managment
bwameth bwameth Fast and accurate alignment of BS-seq reads 2016-09-14 https://github.com/brentp/bwa-meth 0.2.7 bwameth 0.2.7 Up-to-date Sequence Analysis, Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 664 915 8638 12922 740 741 6905 6914 143 143 1525 1525 0 0 0 0 1547 4893 17068 55497 https://dev.workflowhub.eu/workflows/1157?version=2, https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0 epigenetics/methylation-seq
cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program 2022-01-28 https://github.com/ComparativeGenomicsToolkit/cactus 2.7.1 To update Sequence Analysis Multiple sequence alignment, Genome alignment Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics Genomics, Sequence assembly, Mapping, Phylogenetics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. 0 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 73 73 367 367 0 0 0 0 119 119 2456 2456 3 3 11 11 195 585 2834 8502
calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. 2019-08-26 https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold 1.0.0 numpy To update Visualization, Genomic Interval Operations, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
calculate_numeric_param calculate_numeric_param Calculate a numeric parameter value using integer and float values. 2021-05-04 0.1.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 1482 1482 2 2 242 242 0 0 0 0 0 0 0 0 14 42 1724 5172
cami_amber biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments 2024-05-20 https://github.com/CAMI-challenge/AMBER 2.0.7 cami-amber 2.0.7 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber cami-amber AMBER AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. The provided metrics were used in the first community benchmarking challenge of the initiative for the Critical Assessment of Metagenomic Interpretation. 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 8385 8385 0 0 0 0 0 0 0 0 0 0 0 0 13 39 8385 25155 https://usegalaxy.eu/published/workflow?id=20574125a7381fc9, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=b0377f05f97b18b1, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1
cd_hit cd_hit Cluster or compare biological sequence datasets 2018-02-26 http://weizhongli-lab.org/cd-hit/ 4.8.1 cd-hit 4.8.1 Up-to-date Sequence Analysis, Fasta Manipulation Sequence clustering Sequence clustering Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 618 618 12704 12704 1 1 2 2 1 1 2 2 50 50 1025 1025 670 2010 13733 41199 https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5
cemitool cemitool Gene co-expression network analysis tool 2022-10-10 https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html 1.30.0 bioconductor-cemitool 1.30.0 Up-to-date Transcriptomics, RNA, Statistics, Single Cell Enrichment analysis, Pathway or network analysis Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Transcriptomics, Microarray experiment iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 290 290 70 70 452 452 3 3 64 64 0 0 0 0 109 327 806 2418
charts charts Enables advanced visualization options in Galaxy Charts 2018-01-30 https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ 1.0.1 r-getopt To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1626 2016 3490 4417 3691 7220 7785 14556 74 145 195 350 29 29 56 56 5420 20250 11526 42431 https://usegalaxy.eu/published/workflow?id=f30c8054f064ac9f, https://usegalaxy.org/published/workflow?id=cb03300161109123
checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes 2022-07-29 https://github.com/Ecogenomics/CheckM 1.2.3 checkm-genome 1.2.3 Up-to-date Metagenomics Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence assembly validation, Sequence composition calculation, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 1299 1299 9600 9600 75 75 213 213 106 106 799 799 72 72 1352 1352 1552 4656 11964 35892 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5 microbiome/metagenomics-binning
checkm2 checkm2 Rapid assessment of genome bin quality using machine learning 2024-11-08 https://github.com/chklovski/CheckM2 1.0.2 checkm2 1.1.0 To update Metagenomics Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence assembly validation, Sequence composition calculation, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/blob/main/tools/checkm2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2 checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 genome-annotation/bacterial-genome-quality-control
cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions 2022-12-09 https://github.com/BackofenLab/Cherri 0.7 cherri 0.8 To update Transcriptomics, RNA Molecular interactions, pathways and networks, Structure analysis, Machine learning Molecular interactions, pathways and networks, Structure analysis, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1 1 207 207 0 0 0 0 0 0 0 0 0 0 0 0 1 3 207 621
chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm 2024-04-13 https://github.com/B-UMMI/chewBBACA/tree/master chewbbaca 3.3.10 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 141 141 1302 1302 0 0 0 0 0 0 0 0 0 0 0 0 141 423 1302 3906
chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data 2020-01-19 https://github.com/pavanvidem/chira 1.4.3 chira 1.4.3 Up-to-date RNA, Transcriptomics, Sequence Analysis RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 310 310 29825 29828 130 130 12702 12702 17 17 330 330 0 0 0 0 457 1371 42857 128574 https://dev.workflowhub.eu/workflows/1291?version=2, https://usegalaxy.eu/published/workflow?id=25a209bda998412f, https://usegalaxy.eu/published/workflow?id=26c4882e320ed7b3, https://usegalaxy.eu/published/workflow?id=66834f10c86362b9, https://workflowhub.eu/workflows/66?version=1, https://workflowhub.eu/workflows/67?version=1 transcriptomics/rna-interactome
chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing 2023-01-18 https://github.com/cumbof/chopin2 1.0.9.post1 chopin2 To update Machine Learning iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 17 17 0 0 0 0 0 0 0 0 7 21 17 51 statistics/hyperdimensional_computing
chromeister chromeister ultra-fast pairwise genome comparisons 2020-09-30 https://github.com/estebanpw/chromeister 1.5.a chromeister 1.5.a Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 470 470 9192 9192 0 0 0 0 224 224 1493 1493 55 55 2423 2423 749 2247 13108 39324 https://dev.workflowhub.eu/workflows/1004?version=1, https://dev.workflowhub.eu/workflows/1128?version=1, https://dev.workflowhub.eu/workflows/1156?version=1, https://usegalaxy.org.au/published/workflow?id=478c79365fc9677f, https://usegalaxy.org.au/published/workflow?id=7f37c5366bce5489, https://usegalaxy.org.au/published/workflow?id=d06665e4bc7fff6d, https://usegalaxy.org.au/published/workflow?id=d957bfeb3cd03db0 assembly/assembly-quality-control, genome-annotation/hpc-for-lsgc
circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. 2022-08-26 https://github.com/YangLab/CIRCexplorer2 2.3.8 circexplorer2 2.3.8 Up-to-date RNA, Assembly RNA splicing, Gene transcripts, Literature and language RNA splicing, Gene transcripts, Literature and language iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 37 37 806 806 0 0 0 0 0 0 0 0 0 0 0 0 37 111 806 2418
circos circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy 2017-08-07 http://circos.ca/ 0.69.8 circos 0.69.9 To update Graphics Sequence visualisation Sequence visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. 11 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 11 11 0 0 0 0 0 0 11 0 0 0 0 0 11 11 11 0 2757 2822 28546 29368 3797 3923 34138 34638 1027 1051 26702 27064 75 75 571 571 7656 23183 89957 271555 https://dev.workflowhub.eu/workflows/1118?version=1, https://dev.workflowhub.eu/workflows/1248?version=2, https://dev.workflowhub.eu/workflows/1249?version=2, https://dev.workflowhub.eu/workflows/1253?version=1, https://dev.workflowhub.eu/workflows/1337?version=1, https://dev.workflowhub.eu/workflows/630?version=1, https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=75e88603745e069e, https://usegalaxy.eu/published/workflow?id=b1d1694b95ed10e1, https://usegalaxy.org.au/published/workflow?id=0f9a29e8eac2075c, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=6588e175004aba38, https://usegalaxy.org.au/published/workflow?id=6a58898d37da5c83, https://usegalaxy.org.au/published/workflow?id=f85353f93461d180, https://workflowhub.eu/workflows/676?version=1 assembly/ecoli_comparison, variant-analysis/somatic-variant-discovery, visualisation/circos, visualisation/circos-microbial
cite_seq_count cite_seq_count Count CMO/HTO 2023-01-18 https://github.com/Hoohm/CITE-seq-Count 1.4.4 cite-seq-count 1.4.5 To update Single Cell, Transcriptomics, Proteomics RNA-Seq quantification RNA-Seq quantification Transcriptomics, Immunoproteins and antigens Transcriptomics, Immunoproteins and antigens iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 21 21 5 5 9 9 1 1 144 144 0 0 0 0 10 30 174 522 https://usegalaxy.eu/published/workflow?id=4cb8f782994763a4, https://usegalaxy.eu/published/workflow?id=6ed089fe65347272, https://usegalaxy.eu/published/workflow?id=865715636d40b798, https://usegalaxy.eu/published/workflow?id=a72e3cb6eb656102, https://usegalaxy.eu/published/workflow?id=c4327bccfa623f7e, https://usegalaxy.org.au/published/workflow?id=0f01e24e6c33a834, https://usegalaxy.org.au/published/workflow?id=aa387984ac9e2f71, https://usegalaxy.org.au/published/workflow?id=b09530351a9e9ffb, https://usegalaxy.org.au/published/workflow?id=b88036506d0be117, https://usegalaxy.org.au/published/workflow?id=bcdbefda8e15e547, https://usegalaxy.org/published/workflow?id=1d19cf599e1d4a0f, https://usegalaxy.org/published/workflow?id=586b923221fb5da4, https://usegalaxy.org/published/workflow?id=90ac9dc2bd9d8092, https://usegalaxy.org/published/workflow?id=a737766dd083b280, https://workflowhub.eu/workflows/694?version=6
clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling 2022-06-15 https://github.com/HKU-BAL/Clair3 1.0.10 clair3 1.1.1 To update Sequence Analysis, Variant Analysis Variant calling Variant calling Molecular genetics Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 242 242 4369 4369 21 21 547 547 8 8 165 165 0 0 0 0 271 813 5081 15243 https://dev.workflowhub.eu/workflows/1083?version=1, https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869, https://usegalaxy.eu/published/workflow?id=64abcddeb516a712, https://usegalaxy.eu/published/workflow?id=cb54883452a73019, https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f, https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc, https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad, https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba, https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f, https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6, https://usegalaxy.org/published/workflow?id=6d778eeb176d563c, https://workflowhub.eu/workflows/1063?version=3 microbiome/pathogen-detection-from-nanopore-foodborne-data
clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins 2022-10-02 http://www.clustal.org/clustal2/ 2.1 clustalw 2.1 Up-to-date Phylogenetics, Sequence Analysis Multiple sequence alignment Multiple sequence alignment Phylogeny, Sequence analysis Phylogeny, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1879 2012 89195 90338 3880 7737 53695 93366 720 796 10072 11520 35 35 662 662 6514 23608 153624 503134 https://dev.workflowhub.eu/workflows/1077?version=2, https://dev.workflowhub.eu/workflows/1160?version=2, https://dev.workflowhub.eu/workflows/1264?version=2, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=3e0246389fb70340, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=7b68f97bf88f99b9, https://usegalaxy.org/published/workflow?id=87685c6247521b54, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=b06c96cb684e30a4, https://usegalaxy.org/published/workflow?id=be9bd7286d38c210, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/358?version=1 ecology/phylogeny-data-prep, genome-annotation/hpc-for-lsgc, microbiome/pathogen-detection-from-nanopore-foodborne-data
clustering_from_distmat clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy 2024-08-08 https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ 1.1.1 python To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22 123 123 0 0 0 0 0 0 0 0 0 0 0 0 22 66 123 369 evolution/mtb_transmission
cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. 2024-02-27 https://pypi.org/project/cnv-phenopacket/ 2.0.0 cnv-vcf2json To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 13 13 0 0 0 0 0 0 0 0 0 0 0 0 7 21 13 39 variant-analysis/beaconise_1000hg
cnv_phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. 2024-02-27 https://pypi.org/project/cnv-phenopacket/ 1.0.2 cnv-phenopacket To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 7 7 0 0 0 0 0 0 0 0 0 0 0 0 5 15 7 21 variant-analysis/beaconise_1000hg
cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_export_bed, cnvkit_breaks, cnvkit_call, cnvkit_export_cdt, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_export_jtv, cnvkit_export_nexus_basic, cnvkit_export_nexus_ogt, cnvkit_reference, cnvkit_scatter, cnvkit_export_seg, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target, cnvkit_theta, cnvkit_export_vcf detecting copy number variants and alterations genome-wide from high-throughput sequencing 2023-03-14 https://github.com/etal/cnvkit 0.9.12 cnvkit 0.9.12 Up-to-date Variant Analysis Variant calling Variant calling DNA structural variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. 0 25 25 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 255 255 1130 1130 0 0 0 0 0 0 0 0 0 0 0 0 255 765 1130 3390
codeml codeml Detects positive selection 2017-07-19 http://abacus.gene.ucl.ac.uk/software/paml.html 4.9 paml 4.10.7 To update Phylogenetics Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Probabilistic sequence generation Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 66 73 62315 62370 0 0 0 0 0 0 0 0 0 0 0 0 66 205 62315 187000
cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons 2022-08-11 https://github.com/cbg-ethz/cojac 0.9.3 cojac 0.9.3 Up-to-date Metagenomics, Sequence Analysis Genetic variation Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 23 23 2759 2759 10 10 20 20 0 0 0 0 0 0 0 0 33 99 2779 8337 https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b
colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 2024-03-24 https://github.com/sokrypton/ColabFold 1.5.5 To update Proteomics, Graphics Database search, Protein structure prediction, Fold recognition Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 296 296 9177 9177 0 0 0 0 0 0 0 0 296 888 9177 27531
colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome 2017-10-02 https://colibread.inria.fr/ 24.7.14 commet 24.7.14 Up-to-date Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 43 44 1362 1364 0 0 0 0 0 0 0 0 68 68 259 262 111 334 1621 4868
collection_column_join collection_column_join Column Join on Collections 2016-05-26 https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join 0.0.3 coreutils 8.25 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 4310 4568 25785 27569 4957 5592 22463 27003 778 816 3186 3399 720 720 3392 3392 10765 33226 54826 171015 https://dev.workflowhub.eu/workflows/1077?version=2, https://dev.workflowhub.eu/workflows/1087?version=2, https://dev.workflowhub.eu/workflows/1103?version=1, https://dev.workflowhub.eu/workflows/1120?version=1, https://dev.workflowhub.eu/workflows/1218?version=1, https://dev.workflowhub.eu/workflows/1295?version=1, https://dev.workflowhub.eu/workflows/1332?version=1, https://dev.workflowhub.eu/workflows/1391?version=1, 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https://workflowhub.eu/workflows/641?version=16, https://workflowhub.eu/workflows/642?version=14, https://workflowhub.eu/workflows/689?version=1, https://workflowhub.eu/workflows/698?version=1, https://workflowhub.eu/workflows/751?version=9, https://workflowhub.eu/workflows/789?version=1, https://workflowhub.eu/workflows/794?version=2 assembly/vgp_genome_assembly, data-science/data-manipulation-olympics, digital-humanities/text_mining_chinese, genome-annotation/gene-centric, genome-annotation/tnseq, introduction/data-manipulation-olympics, introduction/galaxy-intro-peaks2genes, microbiome/dada-16S, microbiome/metaplasmidome_query, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/maxquant-label-free, single-cell/bulk-deconvolution-evaluate, transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways, variant-analysis/pox-tiled-amplicon
column_order_header_sort column_order_header_sort Sort Column Order by heading 2017-04-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort 0.0.1 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 270 311 4403 4606 400 400 1969 1970 0 0 0 0 13 13 20 20 683 2090 6392 19380 https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=93650de42fb8c015, https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8
column_remove_by_header column_remove_by_header Remove columns by header 2017-04-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header 1.0 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 745 809 9250 9882 784 791 5535 5546 29 29 2020 2020 37 37 179 179 1595 4856 16984 51595 https://dev.workflowhub.eu/workflows/1230?version=1, https://dev.workflowhub.eu/workflows/1395?version=1, https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=1b72af1870c540d6, https://usegalaxy.eu/published/workflow?id=2ae4a83327615155, https://usegalaxy.eu/published/workflow?id=409ac72c9906f16a, https://usegalaxy.eu/published/workflow?id=9791e8aae12d6e63, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809, https://usegalaxy.eu/published/workflow?id=d1b3b62e7f91e217, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.org/published/workflow?id=13a3954b8894e1b1, https://usegalaxy.org/published/workflow?id=3cb4fd9ff755d36e, https://workflowhub.eu/workflows/1207?version=2, https://workflowhub.eu/workflows/888?version=2 ecology/ecoregiolifetraits, single-cell/bulk-music-3-preparebulk, single-cell/pseudobulk-analysis
compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO 2023-12-04 https://github.com/huangnengCSU/compleasm 0.2.6 compleasm 0.2.7 To update Sequence Analysis Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Sequence assembly, Transcriptomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm compleasm compleasm "Compleasm: a faster and more accurate reimplementation of BUSCO" 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 59 59 475 475 52 52 104 104 8 8 54 54 12 12 362 362 131 393 995 2985 https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=7de6e20699183cd3, https://usegalaxy.eu/published/workflow?id=9fb31a16b258cc1a, https://usegalaxy.fr/published/workflow?id=2c823ac083c3cb6d, https://usegalaxy.fr/published/workflow?id=55be36ab73515e65, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6
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microbiome/pathogen-detection-from-nanopore-foodborne-data, variant-analysis/pox-tiled-amplicon
compress_file compress_file Compress files. 2022-02-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file 0.1.0 gzip To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 329 329 7583 7583 388 388 5749 5749 73 73 12589 12589 0 0 0 0 790 2370 25921 77763 https://dev.workflowhub.eu/workflows/1360?version=1, https://usegalaxy.eu/published/workflow?id=2062c7e1c50b05f3, https://usegalaxy.eu/published/workflow?id=c7f34c67c9054234, https://usegalaxy.org.au/published/workflow?id=614898119cf0dabf, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org/published/workflow?id=982a3eb2b4c4f5ae, https://workflowhub.eu/workflows/738?version=1 assembly/mitochondrion-assembly
concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. 2022-02-18 https://github.com/BinPro/CONCOCT 1.1.0 concoct 1.1.0 Up-to-date Metagenomics Sequence clustering, Read binning Sequence clustering, Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. 5 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 221 221 5424 5424 0 0 0 0 0 0 0 0 10 10 2946 2946 231 693 8370 25110 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=58f779d238d569dc, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=b0377f05f97b18b1
contig_annotation_tool cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) 2019-11-27 https://github.com/dutilh/CAT 5.2.3 cat 6.0.1 To update Metagenomics Taxonomic classification, Sequence assembly, Coding region prediction Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. 5 2 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 662 668 16563 16609 542 542 1592 1592 108 108 693 693 0 0 0 0 1312 3942 18848 56590 https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef
control_freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. 2020-07-22 http://boevalab.inf.ethz.ch/FREEC/ 11.6 gawk To update Variant Analysis Copy number estimation, Variant calling, Genome alignment Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining Oncology, Human genetics, Data mining iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 102 102 1432 1432 0 0 0 0 3 3 96 96 0 0 0 0 105 315 1528 4584 https://dev.workflowhub.eu/workflows/1118?version=1, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=75e88603745e069e, https://usegalaxy.eu/published/workflow?id=7cc253b53379b727, https://usegalaxy.eu/published/workflow?id=b1d1694b95ed10e1, https://workflowhub.eu/workflows/676?version=1 variant-analysis/somatic-variant-discovery
cosg cosg Marker gene identification for single-cell sequencing data using COSG. 2024-05-29 https://github.com/genecell/COSG 1.0.1 cosg 1.0.3 To update Transcriptomics, Sequence Analysis, Single Cell Nucleic acid sequence analysis Nucleic acid sequence analysis Bioinformatics Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg cosg COSG COSG is a cosine similarity-based method for more accurate and scalable marker gene identification. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file 2017-10-16 https://github.com/galaxyproject/tools-iuc 0.0.4 perl-number-format 1.76 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
coverm coverm_contig, coverm_genome CoverM genome and contig wrappers 2022-04-26 https://github.com/wwood/CoverM 0.7.0 coverm 0.7.0 Up-to-date Sequence Analysis Local alignment Local alignment Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm coverm CoverM Read coverage calculator for metagenomics 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 194 194 1450 1450 0 0 0 0 0 0 0 0 6 6 467 467 200 600 1917 5751 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=d57d41e306241396 assembly/metagenomics-assembly, microbiome/metagenomics-assembly
crispr_studio crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. 2019-08-13 https://github.com/moineaulab/CRISPRStudio 1+galaxy0 crispr_studio 1 To update Sequence Analysis Visualisation Visualisation Sequence analysis, Genomics, Data visualisation Sequence analysis, Genomics, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 80 82 2072 2090 0 0 0 0 0 0 0 0 0 0 0 0 80 242 2072 6234
crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool 2018-07-27 https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 To update Transcriptomics, Visualization, Single Cell Filtering, Sequence contamination filtering, Sequencing quality control, RNA-Seq analysis Filtering, Sequence contamination filtering, RNA-Seq analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter cross-contamination_barcode_filter Cross-contamination Barcode Filter This tool produces plots enabling the discovery of cross-contamination of samples across the full selection of barcodes used in a sequencing plate. It also filters false barcodes from each batch and retains only the 'real' barcodes. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 97 216 412 48 48 141 141 0 0 0 0 0 0 0 0 123 391 357 1267
crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies 2016-04-04 http://crossmap.sourceforge.net/ 0.7.0 crossmap 0.7.0 Up-to-date Convert Formats, Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 5 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 5 6 5 0 341 358 2197 2340 948 952 5406 5415 0 0 0 0 0 0 0 0 1289 3888 7603 22961
cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 1 0 0 0 1 1 1 0 171 307 773 1229 692 5769 2030 25038 44 98 234 493 65 65 310 328 972 8183 3347 33782 https://usegalaxy.org/published/workflow?id=2ae1b71ea4634d1e, https://usegalaxy.org/published/workflow?id=2b1c98865a3ce11a, https://usegalaxy.org/published/workflow?id=3771c5db96f8f246, https://usegalaxy.org/published/workflow?id=52a2cca52985cdc7, https://usegalaxy.org/published/workflow?id=61b7ad6588f7db41, https://usegalaxy.org/published/workflow?id=684ff8ee49c7f116, https://usegalaxy.org/published/workflow?id=712d9ae42b45c4b9, https://usegalaxy.org/published/workflow?id=7c3b5398dd05a6a5, https://usegalaxy.org/published/workflow?id=82681bd5f059e39a, https://usegalaxy.org/published/workflow?id=930dfd894899173e, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=b4174fd0cf4f865c, https://usegalaxy.org/published/workflow?id=eae740bac11ecc91, https://usegalaxy.org/published/workflow?id=f47f0b25c1405128, https://usegalaxy.org/published/workflow?id=fcce98489c8ca7a3
cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 561 774 3571 6257 4588 20492 21851 117882 101 616 712 4231 1 1 4 4 5251 32385 26138 180650 https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=60f2a8721e203057, https://usegalaxy.org.au/published/workflow?id=0427bd5f28789a1f, https://usegalaxy.org.au/published/workflow?id=115896e8f4059e44, https://usegalaxy.org.au/published/workflow?id=126116a92f2e9a68, https://usegalaxy.org.au/published/workflow?id=1624a678c6791ca6, https://usegalaxy.org.au/published/workflow?id=189c584ea4bde59a, 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cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 1 0 0 0 1 1 1 0 908 1301 26309 34334 6500 27355 65979 352609 366 844 3635 10341 44 45 1007 1051 7818 45181 96930 592195 https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=0eb137cd936bbfe0, https://usegalaxy.eu/published/workflow?id=249c5d6698c8b98c, https://usegalaxy.eu/published/workflow?id=2d08a73dd8ff99e9, https://usegalaxy.eu/published/workflow?id=406e6ef0dfb38628, https://usegalaxy.eu/published/workflow?id=409336bf210033a2, https://usegalaxy.eu/published/workflow?id=5be158931abca947, 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cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 1 1 1 0 369 677 2352 3561 3243 13839 18831 68029 173 573 1115 3076 57 57 128 128 3842 22830 22426 119646 https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=60f2a8721e203057, https://usegalaxy.org.au/published/workflow?id=0427bd5f28789a1f, https://usegalaxy.org.au/published/workflow?id=115896e8f4059e44, https://usegalaxy.org.au/published/workflow?id=126116a92f2e9a68, https://usegalaxy.org.au/published/workflow?id=1624a678c6791ca6, https://usegalaxy.org.au/published/workflow?id=189c584ea4bde59a, https://usegalaxy.org.au/published/workflow?id=1ac197bae296b2bf, https://usegalaxy.org.au/published/workflow?id=2a97585556d53a43, https://usegalaxy.org.au/published/workflow?id=39bb22274ede7500, https://usegalaxy.org.au/published/workflow?id=427e27f87b8048a3, https://usegalaxy.org.au/published/workflow?id=50fdbdb8f807c021, https://usegalaxy.org.au/published/workflow?id=52d2fb868defa474, https://usegalaxy.org.au/published/workflow?id=581c455f74aa55a4, https://usegalaxy.org.au/published/workflow?id=60c5675ed2f4a7d8, https://usegalaxy.org.au/published/workflow?id=79572be1bf642251, https://usegalaxy.org.au/published/workflow?id=7a63fff9a122e60c, https://usegalaxy.org.au/published/workflow?id=80a1493fb9593bb3, https://usegalaxy.org.au/published/workflow?id=84589f66ec87ad99, https://usegalaxy.org.au/published/workflow?id=89531196e32e330e, https://usegalaxy.org.au/published/workflow?id=9176f8ebac92d10c, https://usegalaxy.org.au/published/workflow?id=9beae9b0c863d335, https://usegalaxy.org.au/published/workflow?id=a3efc48b5992374e, https://usegalaxy.org.au/published/workflow?id=b2818098da6e2f82, https://usegalaxy.org.au/published/workflow?id=b518ee5540ed01fd, https://usegalaxy.org.au/published/workflow?id=cc6de673126c56cb, https://usegalaxy.org.au/published/workflow?id=d0933b5040adf902, https://usegalaxy.org.au/published/workflow?id=d1b604a5441dc4b0, https://usegalaxy.org.au/published/workflow?id=d2073964dbe9acfa, https://usegalaxy.org.au/published/workflow?id=d3989c6c2c663cd3, https://usegalaxy.org.au/published/workflow?id=d42df3bb51a94a52, https://usegalaxy.org.au/published/workflow?id=d68e167c3423c795, https://usegalaxy.org.au/published/workflow?id=d8ee4c7ef846e30f, https://usegalaxy.org.au/published/workflow?id=ec202ccfb5f03d0d, https://usegalaxy.org.au/published/workflow?id=fd1b3d7f2d34ff09, https://usegalaxy.org/published/workflow?id=035c28a247976f2c, https://usegalaxy.org/published/workflow?id=07e4414905458c86, https://usegalaxy.org/published/workflow?id=10fa713ca3076a47, https://usegalaxy.org/published/workflow?id=17beb47e45a7690c, https://usegalaxy.org/published/workflow?id=207b8de8509c572c, https://usegalaxy.org/published/workflow?id=2566f7c6bef19b18, https://usegalaxy.org/published/workflow?id=2ae1b71ea4634d1e, https://usegalaxy.org/published/workflow?id=2b1c98865a3ce11a, https://usegalaxy.org/published/workflow?id=3771c5db96f8f246, https://usegalaxy.org/published/workflow?id=45d37579deee182c, https://usegalaxy.org/published/workflow?id=462261c5e22635f0, https://usegalaxy.org/published/workflow?id=52a2cca52985cdc7, https://usegalaxy.org/published/workflow?id=58ce6470337a190d, https://usegalaxy.org/published/workflow?id=5aa2caa2dcae1477, https://usegalaxy.org/published/workflow?id=712d9ae42b45c4b9, https://usegalaxy.org/published/workflow?id=794e7e952003d3d9, https://usegalaxy.org/published/workflow?id=82681bd5f059e39a, https://usegalaxy.org/published/workflow?id=87fab09e4c592435, https://usegalaxy.org/published/workflow?id=8b2c8c8ce121177d, https://usegalaxy.org/published/workflow?id=930dfd894899173e, https://usegalaxy.org/published/workflow?id=a036991efb5503ab, https://usegalaxy.org/published/workflow?id=aae5b6d9beb860ba, https://usegalaxy.org/published/workflow?id=adaa12b855e4c336, https://usegalaxy.org/published/workflow?id=b4174fd0cf4f865c, https://usegalaxy.org/published/workflow?id=c64719e91e7346a2, https://usegalaxy.org/published/workflow?id=d69ea491b99016f4, https://usegalaxy.org/published/workflow?id=d72e33effe07de02, https://usegalaxy.org/published/workflow?id=df7459b7e8acb872, https://usegalaxy.org/published/workflow?id=e7bfa3c733835b22, https://usegalaxy.org/published/workflow?id=eae740bac11ecc91, https://usegalaxy.org/published/workflow?id=f47f0b25c1405128, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/40?version=1
cuffnorm cuffnorm The Cuffnorm tool 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 74 116 332 706 239 1172 841 13511 52 70 280 341 0 0 0 0 365 2088 1453 17464
cuffquant cuffquant The Cuffquant tool 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 51 76 390 757 251 1321 1607 15913 26 47 287 423 0 0 0 0 328 2100 2284 21661 https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.org/published/workflow?id=8b2c8c8ce121177d, https://workflowhub.eu/workflows/40?version=1
cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). 2018-02-20 https://cutadapt.readthedocs.org/en/stable/ 5.1 cutadapt 5.1 Up-to-date Fasta Manipulation, Fastq Manipulation, Sequence Analysis Sequence trimming, Primer removal, Read pre-processing Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Genomics, Probes and primers, Sequencing lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 12789 14098 283597 301862 20522 22709 359429 406336 3719 3921 69969 73269 1360 1361 36413 36423 38390 118869 749408 2316706 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assembly/vgp_genome_assembly, contributing/create-new-tutorial, ecology/ENA_Biodiv_submission, epigenetics/atac-seq, genome-annotation/crispr-screen, genome-annotation/tnseq, microbiome/metagenomics-assembly, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, sequence-analysis/quality-control, transcriptomics/clipseq, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-interactome, transcriptomics/rna-seq-reads-to-counts
cutesv cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. 2020-09-23 https://github.com/tjiangHIT/cuteSV 2.1.2 cutesv 2.1.2 Up-to-date Variant Analysis Split read mapping, Genotyping, Structural variation detection Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science Sequencing, Computer science iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 51 51 283 283 0 0 0 0 11 11 141 141 0 0 0 0 62 186 424 1272
cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. 2015-12-18 1.1.1 matplotlib To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 83 127 281 0 0 0 0 0 0 0 0 38 159 127 535
dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_primerCheck, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers 2019-07-05 https://benjjneb.github.io/dada2/index.html 1.34.0 bioconductor-dada2 1.34.0 Up-to-date Metagenomics Variant calling, DNA barcoding Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics Sequencing, Genetic variation, Microbial ecology, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. 10 10 11 10 0 0 0 0 0 0 0 0 0 0 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 10 10 0 3832 3854 120579 120969 6324 6335 211412 211497 611 611 20111 20111 273 273 26613 26613 11040 33153 378715 1136620 https://dev.workflowhub.eu/workflows/1105?version=2, https://usegalaxy.eu/published/workflow?id=48d0dc424e71d8c2, https://usegalaxy.eu/published/workflow?id=642f4c47028031d7, https://usegalaxy.eu/published/workflow?id=b483cf6a138d2372, https://usegalaxy.eu/published/workflow?id=e132370adf8f2838, https://usegalaxy.fr/published/workflow?id=b5d86d505c09d170, https://usegalaxy.org.au/published/workflow?id=1016f17b77a8216d, https://usegalaxy.org.au/published/workflow?id=400fbd96fb04c60e, https://usegalaxy.org/published/workflow?id=4faff660f6defa10, https://usegalaxy.org/published/workflow?id=5df593510c7d944d, https://usegalaxy.org/published/workflow?id=78e60413358273bc, https://usegalaxy.org/published/workflow?id=806ef8816168916f, https://usegalaxy.org/published/workflow?id=e067c4e66f0af362, https://usegalaxy.org/published/workflow?id=ecf3a7f9da7409ef, https://workflowhub.eu/workflows/790?version=2 microbiome/dada-16S
das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics 2022-06-23 https://github.com/cmks/DAS_Tool 1.1.7 das_tool 1.1.7 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 67 67 4440 4440 1 1 7 7 0 0 0 0 3 3 1080 1080 71 213 5527 16581 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=b0377f05f97b18b1
data_manager_homer_preparse homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. 2021-08-08 http://homer.ucsd.edu/homer/index.html 4.11 homer 5.1 To update Sequence Analysis Sequence motif discovery Sequence motif discovery iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 770 770 9800 9800 0 0 0 0 0 0 0 0 46 47 341 487 816 2449 10141 30569 https://usegalaxy.eu/published/workflow?id=d3a4e6cc1b4565e5
data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool 2016-02-18 1.0.0 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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decontam decontam Removes decontamination features (ASVs/OTUs) using control samples 2024-09-13 https://github.com/benjjneb/decontam 1.22.0 bioconductor-decontam 1.26.0 To update Metagenomics Classification Classification Metagenomics, Microbial ecology, Sequencing Metagenomics, Microbial ecology, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam decontam decontam Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 3 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264
decontaminator decontaminator Deep Learning method for novel virus detection in sequencing data 2023-01-09 https://github.com/cbib/decontaminator 1.0.0 numpy To update Machine Learning Filtering Filtering Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator decontaminator decontaminator Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 34 34 136 136 0 0 0 0 0 0 0 0 0 0 0 0 34 102 136 408
deeparg deeparg_predict, deeparg_short_reads A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes 2024-10-07 https://github.com/gaarangoa/deeparg 1.0.4 deeparg 1.0.4 Up-to-date Sequence Analysis Antimicrobial resistance prediction, Antimicrobial resistance prediction Antimicrobial resistance prediction, Antimicrobial resistance prediction Microbiology Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deeparg https://github.com/galaxyproject/tools-iuc/tree/main/tools/deeparg deeparg DeepARG A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
deepmicro deepmicro Representation learning and classification framework 2023-03-16 https://github.com/paulzierep/DeepMicro 1.4 deepmicro 1.4 Up-to-date Machine Learning Essential dynamics, Splitting, Community profiling Essential dynamics, Splitting Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 559 559 0 0 0 0 0 0 0 0 0 0 0 0 8 24 559 1677
deepsig deepsig Predictor of signal peptides in proteins based on deep learning 2023-04-28 https://github.com/BolognaBiocomp/deepsig 1.2.5 deepsig 1.2.5 Up-to-date Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 83 173 173 0 0 0 0 0 0 0 0 5 5 9 9 88 264 182 546 https://usegalaxy.eu/published/workflow?id=a018307be3563f28
deepvariant deepvariant DeepVariant is a deep learning-based variant caller 2021-09-06 https://github.com/google/deepvariant 1.5.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 401 401 4137 4137 599 599 4146 4146 0 0 0 0 0 0 0 0 1000 3000 8283 24849 https://usegalaxy.org/published/workflow?id=39753cc73284963f, https://usegalaxy.org/published/workflow?id=b1a98a2d5ebda1c5, https://usegalaxy.org/published/workflow?id=e7586d70715207b5
deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables 2018-11-22 https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate 1.1.0 bedtools 2.31.1 To update Transcriptomics, Single Cell RNA-Seq analysis, Gene functional annotation RNA-Seq analysis, Gene functional annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate deg_annotate DEG Annotate This tool appends the output table of DESeq2 or DEXSeq with gene symbols, biotypes, positions etc. The information you want to add is configurable. 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delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. 2020-09-28 https://github.com/dellytools/delly 0.9.1 delly 1.3.3 To update Variant Analysis Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis Indel detection, Structural variation detection, Genotyping DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 6 0 0 0 0 0 6 6 0 0 340 340 1823 1823 0 0 0 0 0 0 0 0 0 0 0 0 340 1020 1823 5469
deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution 2014-12-03 https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html 2.11.40.8 bioconductor-deseq2 1.46.0 To update Transcriptomics, RNA, Statistics, Single Cell Differential gene expression analysis, RNA-Seq analysis Differential gene expression analysis, RNA-Seq analysis RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. 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dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq 2015-09-25 https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html 1.48.0 bioconductor-dexseq 1.52.0 To update Transcriptomics, RNA, Statistics, Single Cell Enrichment analysis, Exonic splicing enhancer prediction Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 522 862 14762 17581 1283 2619 17846 29794 143 168 3836 4518 11 11 95 95 1959 7578 36539 125066 https://usegalaxy.org/published/workflow?id=82681bd5f059e39a transcriptomics/ref-based
diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. 2021-03-21 https://github.com/bbuchfink/diamond 2.1.11 diamond 2.1.12 To update Sequence Analysis Sequence alignment analysis Sequence alignment analysis Sequence analysis, Proteins Sequence analysis, Proteins bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 0 1 0 0 0 0 0 0 0 0 0 0 3 3 0 2052 2133 64013 64783 1195 1698 23835 30041 598 598 64629 64629 221 221 2055 2073 4066 12782 154532 470590 https://dev.workflowhub.eu/workflows/1127?version=3, https://dev.workflowhub.eu/workflows/1173?version=2, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=ff4d5beb6ce1809d, https://usegalaxy.org.au/published/workflow?id=0a3fb089674de144, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 assembly/ERGA-post-assembly-QC, genome-annotation/functional, genome-annotation/gene-centric, sequence-analysis/ncbi-blast-against-the-madland
diffbind diffbind Diffbind provides functions for processing ChIP-Seq data. 2018-01-21 http://bioconductor.org/packages/release/bioc/html/DiffBind.html 3.12.0 bioconductor-diffbind 3.16.0 To update ChIP-seq Differential binding analysis Differential binding analysis ChIP-seq ChIP-seq bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 637 704 7747 8575 1327 1996 14222 19463 78 93 1812 2039 66 66 117 117 2108 7075 23898 77990 https://usegalaxy.eu/published/workflow?id=719314fa5263b501, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf
dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. 2023-07-19 https://github.com/cbib/DIMet 0.2.4 dimet 0.2.4 Up-to-date Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler 2017-10-26 http://disco.omicsbio.org/ disco 1.2 To update Metagenomics, Assembly Protein sequence analysis Protein sequence analysis Structure determination Structure determination iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 128 150 345 427 412 413 1443 1449 0 0 0 0 0 0 0 0 540 1643 1788 5452
dnabot dnabot DNA assembly using BASIC on OpenTrons 2022-04-17 https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT 3.1.0 dnabot To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://dev.workflowhub.eu/workflows/1147?version=2 synthetic-biology/basic_assembly_analysis
dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. 2022-12-08 https://github.com/Edinburgh-Genome-Foundry/DnaWeaver 1.0.2 dnaweaver_synbiocad 1.0.2 Up-to-date Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function 2022-09-01 https://github.com/WrightonLabCSU/DRAM 1.5.0 dram 1.5.0 Up-to-date Metagenomics Gene functional annotation Gene functional annotation Metagenomics, Biological databases, Molecular genetics Metagenomics, Biological databases, Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 131 131 7707 7707 0 0 0 0 0 0 0 0 0 0 0 0 131 393 7707 23121
drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets 2020-01-06 https://github.com/MrOlm/drep 3.6.2 drep 3.6.2 Up-to-date Metagenomics Genome comparison Genome comparison Metagenomics, Genomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 145 145 1057 1057 0 0 0 0 0 0 0 0 33 33 515 515 178 534 1572 4716 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9 genome-annotation/bacterial-genome-quality-control
dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data 2019-06-04 https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html 1.10.0 bioconductor-dropletutils 1.26.0 To update Single Cell, Sequence Analysis Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics Sequencing, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 450 462 4364 4596 291 291 4874 4874 38 38 1969 1969 26 26 62 62 805 2427 11269 34039 https://dev.workflowhub.eu/workflows/1019?version=1, https://dev.workflowhub.eu/workflows/1020?version=1, https://dev.workflowhub.eu/workflows/1022?version=1, https://dev.workflowhub.eu/workflows/1220?version=3, https://dev.workflowhub.eu/workflows/1247?version=2, https://dev.workflowhub.eu/workflows/1255?version=2, https://usegalaxy.eu/published/workflow?id=0f563f176bb245af, https://usegalaxy.eu/published/workflow?id=3403d5a8a71e0c3c, https://usegalaxy.eu/published/workflow?id=49a6ddcba35bf085, https://usegalaxy.eu/published/workflow?id=6a6e2c2335051fb5, https://usegalaxy.eu/published/workflow?id=704e6c9bc51db49f, https://usegalaxy.eu/published/workflow?id=7d22eea4278570e8, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=90a32c95b60f5221, https://usegalaxy.eu/published/workflow?id=a1cfb476e849fce3, https://usegalaxy.eu/published/workflow?id=a3cb75fd31ba0689, https://usegalaxy.eu/published/workflow?id=af7c349497a75314, https://usegalaxy.eu/published/workflow?id=b5627201bb4f6943, https://usegalaxy.eu/published/workflow?id=d79309343e2a5d62, https://usegalaxy.eu/published/workflow?id=e7494f29c8672f34, https://usegalaxy.org.au/published/workflow?id=10296e860e9ef4bb, https://usegalaxy.org.au/published/workflow?id=281ea78467e73147, https://usegalaxy.org.au/published/workflow?id=3fd10af90a07f771, https://usegalaxy.org.au/published/workflow?id=41b115a9be4b6002, https://usegalaxy.org.au/published/workflow?id=471615c412b305f2, https://usegalaxy.org.au/published/workflow?id=644d8e4c78df8e36, https://usegalaxy.org.au/published/workflow?id=738350fc2ca69c0b, https://usegalaxy.org.au/published/workflow?id=c64dcc1e6a67f3e4, https://usegalaxy.org.au/published/workflow?id=f627023a3401bf9b, https://usegalaxy.org/published/workflow?id=516a2181b41af94e, https://usegalaxy.org/published/workflow?id=69712265fdb10ed5, https://usegalaxy.org/published/workflow?id=8e6d24a14d2908c2, https://usegalaxy.org/published/workflow?id=b73e416c06790ac5, https://usegalaxy.org/published/workflow?id=be7dab2274c1acdd, https://usegalaxy.org/published/workflow?id=cdb6c9c7037a95b2 single-cell/scrna-data-ingest, single-cell/scrna-preprocessing-tenx
drug2cell drug2cell Collection of utility functions for gene group activity evaluation in scanpy. 2025-01-21 https://github.com/Teichlab/drug2cell 0.1.2 drug2cell 0.1.2 Up-to-date Single Cell iuc https://github.com/Teichlab/drug2cell https://github.com/galaxyproject/tools-iuc/tree/main/tools/drug2cell 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
duplex_family_size_distribution fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families 2019-10-24 1.0.2 matplotlib To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 36 38 557 602 0 0 0 0 0 0 0 0 36 110 557 1716
ebi_tools ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases 2016-11-29 http://www.ebi.ac.uk/services/all 0.1.1 six To update Web Services, Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 130 171 250 419 558 560 1454 1461 0 0 0 0 0 0 0 0 688 2107 1704 5288
edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline 2017-09-11 http://bioconductor.org/packages/release/bioc/html/edgeR.html 3.36.0 bioconductor-edger 4.4.0 To update Transcriptomics, RNA, Statistics, Single Cell Differential gene expression analysis Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq Genetics, RNA-Seq, ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 2605 2952 19687 22821 6267 7920 47124 61548 856 935 8185 9283 27 27 165 165 9755 31344 75161 244139 https://dev.workflowhub.eu/workflows/1395?version=1, https://usegalaxy.eu/published/workflow?id=0229f3f3835c2d53, https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809, https://usegalaxy.eu/published/workflow?id=d1b3b62e7f91e217, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.org.au/published/workflow?id=0fc7c14c4d1ac8f5, https://usegalaxy.org/published/workflow?id=03258e0321162584, https://usegalaxy.org/published/workflow?id=13a3954b8894e1b1, https://usegalaxy.org/published/workflow?id=ce232859a466c75c, https://usegalaxy.org/published/workflow?id=d761637d43ee0324, https://workflowhub.eu/workflows/1207?version=2 single-cell/pseudobulk-analysis
ega_download_client pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. 2020-09-02 https://github.com/EGA-archive/ega-download-client 5.0.2 pyega3 5.2.0 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115 115 2756 2756 46 46 153 153 4 4 214 214 0 0 0 0 165 495 3123 9369 https://dev.workflowhub.eu/workflows/1096?version=2, https://usegalaxy.eu/published/workflow?id=b3c0eba755f269b2, https://workflowhub.eu/workflows/363?version=2 variant-analysis/trio-analysis
egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing 2017-12-28 https://bioconductor.org/packages/release/bioc/html/EGSEA.html 1.20.0 bioconductor-egsea 1.34.0 To update Transcriptomics, RNA, Statistics, Single Cell Gene set testing Gene set testing Systems biology Systems biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 365 429 2723 3263 810 810 5488 5488 274 278 2084 2171 0 0 0 0 1449 4415 10295 31512 https://dev.workflowhub.eu/workflows/1316?version=1, https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3 transcriptomics/rna-seq-genes-to-pathways
emboss emboss_needle, emboss_needleall Galaxy wrappers for EMBOSS6 tools 2025-01-17 http://emboss.open-bio.org/ 6.6.0 emboss 6.6.0 Up-to-date Sequence Analysis, Fasta Manipulation Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology Molecular biology, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 6
emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools 2017-01-11 http://emboss.open-bio.org/ 5.0.0 emboss 6.6.0 To update Sequence Analysis, Fasta Manipulation Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology Molecular biology, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 emboss EMBOSS Diverse suite of tools for sequence analysis; 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ena_upload ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 2020-06-10 https://github.com/usegalaxy-eu/ena-upload-cli 0.9.0 ena-upload-cli 0.9.0 Up-to-date Data Export iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 41 41 377 377 0 0 0 0 14 14 1532 1532 0 0 0 0 55 165 1909 5727 https://dev.workflowhub.eu/workflows/1334?version=1, https://usegalaxy.eu/published/workflow?id=924edc19e0653870 galaxy-interface/upload-data-to-ena
enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API 2017-08-05 https://github.com/bebatut/enasearch enasearch 0.2.2 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 372 484 1898 2361 0 0 0 0 0 0 0 0 0 0 0 0 372 1228 1898 6157
ensembl_vep ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions 2022-05-11 https://github.com/Ensembl/ensembl-vep 114.1 ensembl-vep 114.1 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 201 201 3475 3475 0 0 0 0 0 0 0 0 0 0 0 0 201 603 3475 10425 https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=99ad31bf3970ade4, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1
episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python 2023-03-13 https://github.com/colomemaria/epiScanpy 0.3.2 episcanpy 0.4.0 To update Single Cell, Epigenetics Enrichment analysis, Imputation Enrichment analysis, Imputation Epigenomics, Cell biology, DNA Epigenomics, Cell biology, DNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 88 88 1006 1006 49 49 298 298 3 3 385 385 0 0 0 0 140 420 1689 5067 https://dev.workflowhub.eu/workflows/1011?version=1, https://dev.workflowhub.eu/workflows/1012?version=1, https://dev.workflowhub.eu/workflows/1208?version=1, https://dev.workflowhub.eu/workflows/1275?version=1 single-cell/scatac-preprocessing-tenx
ete_treeviewer ete_treeviewer A toolkit for the analysis and visualization of trees. 2024-11-25 http://etetoolkit.org 3.1.3 curl To update Phylogenetics Phylogenetic analysis, Phylogenetic tree editing Phylogenetic tree editing Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ete-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 sequence-analysis/tapscan-streptophyte-algae
evidencemodeler evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. 2024-07-19 https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file 2.1.0 evidencemodeler 2.1.0 Up-to-date Genome annotation Gene prediction Gene prediction Gene expression, Gene structure Gene expression, Gene structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 9 9 0 0 0 0 0 0 0 0 0 0 0 0 5 15 9 27
exomedepth exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data 2019-11-08 https://cran.r-project.org/package=ExomeDepth 1.1.0 r-exomedepth 1.1.16 To update Sequence Analysis, Variant Analysis Sequence analysis, Variant calling, Genotyping, Copy number estimation Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 61 65 515 537 197 197 3101 3101 0 0 0 0 0 0 0 0 258 778 3616 10870
exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. 2018-08-02 https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate 2.4.0 exonerate 2.4.0 Up-to-date Sequence Analysis Pairwise sequence alignment, Protein threading, Genome alignment Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 185 196 1012 1159 199 199 1122 1122 38 38 1068 1068 25 26 525 533 447 1353 3727 11336
export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn 2017-03-03 https://bitbucket.org/CibioCM/export2graphlan/overview 0.20 export2graphlan 0.22 To update Metagenomics Conversion Conversion Taxonomy, Metabolomics, Biomarkers Taxonomy, Metabolomics, Biomarkers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 615 653 5799 6416 186 186 690 690 110 110 572 572 0 0 0 0 911 2771 7061 21800 https://dev.workflowhub.eu/workflows/1088?version=1, https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf microbiome/metatranscriptomics, microbiome/metatranscriptomics-short
extract_genomic_dna Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. 2016-01-14 3.0.3+galaxy3 bx-python 0.13.0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 1 1 0 0 0 0 0 1 1 1 0 853 1006 9217 13157 1985 12103 17797 260224 11 63 103 611 1 3 1 201 2850 18875 27118 328429 https://dev.workflowhub.eu/workflows/1285?version=2, https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=1ee43d90b69829e9, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=4f40ae432d8a4259, https://usegalaxy.eu/published/workflow?id=51cce3b98da3e822, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=6bce1d419a179c50, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=ad4b347f9b68e127, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://usegalaxy.eu/published/workflow?id=d3a8741131485af2, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://usegalaxy.org/published/workflow?id=0ac68ec25f3534da, https://usegalaxy.org/published/workflow?id=28e86ab943c67417, https://usegalaxy.org/published/workflow?id=30507545aa971637, https://usegalaxy.org/published/workflow?id=468c5a8fe7a40778, https://usegalaxy.org/published/workflow?id=4769befb88f653d6, https://usegalaxy.org/published/workflow?id=56530f4d41413832, https://usegalaxy.org/published/workflow?id=6e75ac640853d0dd, https://usegalaxy.org/published/workflow?id=7643e66a9b4e9c11, https://usegalaxy.org/published/workflow?id=7cae620eea6326af, https://usegalaxy.org/published/workflow?id=94de815260acc3a8, https://usegalaxy.org/published/workflow?id=a666aaaa32f62487, https://usegalaxy.org/published/workflow?id=b8fdf05ec7540510, https://usegalaxy.org/published/workflow?id=c92c9d046b394094, https://usegalaxy.org/published/workflow?id=ce2619816ce10220, https://usegalaxy.org/published/workflow?id=e75a7802d2941f31, https://usegalaxy.org/published/workflow?id=ecb279a9114140ab epigenetics/cut_and_run, transcriptomics/clipseq
fairy fairy_cov, fairy_sketch Fast approximate contig coverage for metagenomic binning 2024-12-20 https://github.com/bluenote-1577/fairy 0.5.8 fairy 0.5.8 Up-to-date Metagenomics Read binning, Sequence assembly validation Read binning, Sequence assembly validation Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy fairy fairy fast approximate contig coverage for metagenomic binningFairy computes multi-sample contig coverage for metagenome-assembled genome (MAG) binning.Fairy is used after metagenomic assembly and before binning. It can- Calculate coverage 100x-1000x faster than read alignment (e.g. BWA)- Give comparable bins for multi-sample binning (short read or nanopore reads)- Output formats that are compatible with MetaBAT2, MaxBin2, SemiBin2, and more 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 13 13 0 0 0 0 0 0 0 0 0 0 0 0 3 9 13 39 https://usegalaxy.eu/published/workflow?id=b0377f05f97b18b1
falco falco A high throughput sequence QC analysis tool 2024-04-17 https://github.com/smithlabcode/falco/ 1.2.4 falco 1.2.5 To update Sequence Analysis Sequencing quality control, Visualisation, Read mapping Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging Workflows, Mapping, Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco falco Falco A high-speed FastQC emulation for quality control of sequencing data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 83 6114 6114 0 0 0 0 9 9 84 84 0 0 0 0 92 276 6198 18594 https://dev.workflowhub.eu/workflows/1329?version=5 assembly/mrsa-illumina, ecology/ENA_Biodiv_submission, epigenetics/cut_and_run, epigenetics/methylation-seq, galaxy-interface/workflow-fairification, sequence-analysis/quality-contamination-control, transcriptomics/ref-based, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants
fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) 2019-08-30 https://github.com/fannyhb/fargene 0.1 fargene 0.1 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology, Antimicrobial resistance Metagenomics, Microbiology, Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 135 138 614 631 260 260 1270 1270 0 0 0 0 0 0 0 0 395 1188 1884 5669
fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Graphics, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 11 11 26 26 0 0 0 0 102 132 5509 5759 1 1 1 1 114 372 5536 16858
fasta_formatter cshl_fasta_formatter FASTA Width formatter 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 280 343 11412 11766 467 2070 3879 25920 76 98 729 1162 6 7 45 55 829 4176 16065 71033 https://usegalaxy.eu/published/workflow?id=02f240f6cf72080a, https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f9648091c06171cd, https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe, https://usegalaxy.org/published/workflow?id=4884918895db9af0, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=63db7f52a280bd2d, https://usegalaxy.org/published/workflow?id=9bea2e9f45f07f32, https://usegalaxy.org/published/workflow?id=a808c139402d7b87, https://workflowhub.eu/workflows/1270?version=1, https://workflowhub.eu/workflows/1271?version=1, https://workflowhub.eu/workflows/1272?version=1, https://workflowhub.eu/workflows/517?version=1, https://workflowhub.eu/workflows/518?version=1
fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 77 117 465 845 219 724 2073 5582 19 21 422 478 5 6 11 21 320 1508 2971 12868 https://usegalaxy.org/published/workflow?id=9efb061a87bc9f4d
fasta_nucleotide_color_plot fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. 2016-03-06 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot 1.0.1 openjdk To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 44 51 168 217 152 203 815 1023 0 0 0 0 0 0 0 0 196 646 983 3206
fasta_stats fasta-stats Display summary statistics for a fasta file. 2018-11-21 https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ 2.0 numpy To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3374 3630 51955 53092 4157 4168 32853 32911 2372 2759 16560 19568 134 134 567 567 10037 30765 101935 310008 https://dev.workflowhub.eu/workflows/1005?version=1, https://dev.workflowhub.eu/workflows/1006?version=1, https://dev.workflowhub.eu/workflows/1124?version=1, https://dev.workflowhub.eu/workflows/1131?version=2, https://dev.workflowhub.eu/workflows/1139?version=1, https://dev.workflowhub.eu/workflows/1164?version=2, https://dev.workflowhub.eu/workflows/1170?version=2, https://dev.workflowhub.eu/workflows/1174?version=2, https://dev.workflowhub.eu/workflows/1194?version=2, https://dev.workflowhub.eu/workflows/233?version=1, https://dev.workflowhub.eu/workflows/584?version=1, https://dev.workflowhub.eu/workflows/585?version=1, https://dev.workflowhub.eu/workflows/586?version=1, https://usegalaxy.eu/published/workflow?id=0ebfab0e957b7267, https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=30b514cfb9cce524, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.eu/published/workflow?id=9ddb703e1db13504, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.org.au/published/workflow?id=044b6b475b4db27a, https://usegalaxy.org.au/published/workflow?id=1ad4c47cee851dda, https://usegalaxy.org.au/published/workflow?id=22bd45f60c60a338, https://usegalaxy.org.au/published/workflow?id=2cb16d321a804b1a, https://usegalaxy.org.au/published/workflow?id=36604d0ab0dee988, https://usegalaxy.org.au/published/workflow?id=479c6b0a96ea1610, https://usegalaxy.org.au/published/workflow?id=52065a4100b11184, https://usegalaxy.org.au/published/workflow?id=5b32e2f0d390a4ba, https://usegalaxy.org.au/published/workflow?id=5cd804644a34c8fd, https://usegalaxy.org.au/published/workflow?id=705658f68ae73930, https://usegalaxy.org.au/published/workflow?id=7c343e5b55474d19, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org.au/published/workflow?id=803ef29108e36e58, https://usegalaxy.org.au/published/workflow?id=8abcfe166f1a6cd8, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=b5403e4fff2961f9, https://usegalaxy.org.au/published/workflow?id=c4d23297f6fbf5f3, https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f, https://usegalaxy.org.au/published/workflow?id=d832905fbaf2ca31, https://usegalaxy.org.au/published/workflow?id=df11f09771e73e04, https://usegalaxy.org.au/published/workflow?id=e5dfeff4a3068f36, https://usegalaxy.org.au/published/workflow?id=f2541030f6d70b59, https://usegalaxy.org.au/published/workflow?id=f83a3cda33131fb8, https://usegalaxy.org/published/workflow?id=0602c14704dbe1ff, https://usegalaxy.org/published/workflow?id=65b4051e722228b8, https://usegalaxy.org/published/workflow?id=bff206b4625375bc, https://usegalaxy.org/published/workflow?id=c8d74054c1820087, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43, https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1, https://workflowhub.eu/workflows/1114?version=1, https://workflowhub.eu/workflows/221?version=3, https://workflowhub.eu/workflows/225?version=1, https://workflowhub.eu/workflows/226?version=1, https://workflowhub.eu/workflows/237?version=2, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/750?version=2, https://workflowhub.eu/workflows/794?version=2 assembly/chloroplast-assembly, assembly/debruijn-graph-assembly, assembly/hifi-assembly, assembly/largegenome, genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short, genome-annotation/braker3
fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity 2020-02-17 https://github.com/ParBLiSS/FastANI 1.3 fastani 1.34 To update Sequence Analysis Genome alignment, Sequence similarity search Genome alignment, Sequence similarity search Microbiology, Genetic variation Microbiology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 744 744 24894 24894 0 0 0 0 37 37 1177 1177 51 51 843 843 832 2496 26914 80742 https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75
fastk fastk_fastk, fastk_histex, fastk_logex FastK: A K-mer counter (for HQ assembly data sets) 2024-05-03 https://github.com/thegenemyers/FASTK 1.1.0 fastk 1.1.0 Up-to-date Assembly k-mer counting, Sequence analysis k-mer counting, Sequence analysis Genomics, Sequence analysis Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk fastk FASTK FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode. 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 156 156 6 6 12 12 0 0 0 0 0 0 0 0 25 75 168 504
fastp fastp Fast all-in-one preprocessing for FASTQ files 2018-03-07 https://github.com/OpenGene/fastp 0.24.3 fastp 0.26.0 To update Sequence Analysis Sequencing quality control, Sequence contamination filtering Sequence contamination filtering Sequence analysis, Probes and primers Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 8030 8192 1196298 1200047 12337 12428 466144 467016 2529 2529 92654 92654 225 225 18568 18568 23121 69616 1773664 5325613 https://dev.workflowhub.eu/workflows/1064?version=1, https://dev.workflowhub.eu/workflows/1069?version=2, https://dev.workflowhub.eu/workflows/1074?version=2, https://dev.workflowhub.eu/workflows/1087?version=2, https://dev.workflowhub.eu/workflows/1097?version=1, https://dev.workflowhub.eu/workflows/1115?version=2, https://dev.workflowhub.eu/workflows/1132?version=2, https://dev.workflowhub.eu/workflows/1135?version=2, https://dev.workflowhub.eu/workflows/1144?version=2, https://dev.workflowhub.eu/workflows/1178?version=1, https://dev.workflowhub.eu/workflows/1197?version=2, https://dev.workflowhub.eu/workflows/1324?version=3, https://dev.workflowhub.eu/workflows/132?version=1, 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fastplong fastplong Fastplong is used for ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.). 2025-05-06 https://github.com/OpenGene/fastplong 0.3.0 fastplong 0.3.0 Up-to-date Sequence Analysis, Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastplong https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastplong 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation, Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 237 274 8845 9114 938 3043 52480 76117 76 89 1922 2155 15 15 51 51 1266 5953 63298 214033 https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.org/published/workflow?id=5b2a0da883be03b7, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395
fastq_dl fastq_dl Download FASTQ files from ENA. 2024-11-14 https://github.com/rpetit3/fastq-dl 3.0.1 fastq-dl 3.0.1 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 90 90 23 23 58 58 0 0 0 0 0 0 0 0 38 114 148 444 https://usegalaxy.eu/published/workflow?id=02f90a96d01fed4f, https://workflowhub.eu/workflows/1274?version=1
fastq_filter fastq_filter Filter FASTQ reads by quality score and length 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 752 876 17948 22337 2636 9439 37231 124263 225 309 4973 6321 73 73 246 246 3686 18069 60398 273963 https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c, https://usegalaxy.eu/published/workflow?id=c7f34c67c9054234, https://usegalaxy.eu/published/workflow?id=e271d95a671182ec, https://usegalaxy.eu/published/workflow?id=f39528391f22aab0, https://usegalaxy.eu/published/workflow?id=f9648091c06171cd, https://usegalaxy.org/published/workflow?id=02c9244e2fb060de, https://usegalaxy.org/published/workflow?id=091896754bcc8ec1, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=344a79d4f12d2cff, https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=48adcc44fe62a99c, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=535484d6482b80f4, https://usegalaxy.org/published/workflow?id=61d324b1eca6300e, https://usegalaxy.org/published/workflow?id=85c3a1fc1d3d3df8, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://usegalaxy.org/published/workflow?id=d860749fd34809d7, https://usegalaxy.org/published/workflow?id=ea69f4fbdbb88c71, https://usegalaxy.org/published/workflow?id=fe3d4001499c3f15, https://workflowhub.eu/workflows/1271?version=1, https://workflowhub.eu/workflows/1272?version=1 ecology/ENA_Biodiv_submission
fastq_groomer fastq_groomer Convert between various FASTQ quality formats. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 2831 3358 100541 113228 8822 45341 165562 906976 682 1118 15654 26912 190 192 7648 7736 12525 75059 289405 1633662 https://dev.workflowhub.eu/workflows/1274?version=2, https://dev.workflowhub.eu/workflows/1287?version=2, https://dev.workflowhub.eu/workflows/1292?version=2, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=70b1c40b818cc320, https://usegalaxy.eu/published/workflow?id=7117dbcbd5d12de5, 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https://usegalaxy.org/published/workflow?id=d3eae9943ce2a62b, https://usegalaxy.org/published/workflow?id=d69ea491b99016f4, https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f, https://usegalaxy.org/published/workflow?id=db8443163482a2e0, https://usegalaxy.org/published/workflow?id=dcc7c5fdef8780fd, https://usegalaxy.org/published/workflow?id=df1fa0b73f741a9c, https://usegalaxy.org/published/workflow?id=df6b9760e071b91b, https://usegalaxy.org/published/workflow?id=df6c398b2d4f1e99, https://usegalaxy.org/published/workflow?id=df7459b7e8acb872, https://usegalaxy.org/published/workflow?id=e2432c4d2b61705a, https://usegalaxy.org/published/workflow?id=e2fa6584853a0dee, https://usegalaxy.org/published/workflow?id=e6838c861b6beaed, https://usegalaxy.org/published/workflow?id=eb20150175a6ab03, https://usegalaxy.org/published/workflow?id=f2465afbdfc8ad46, https://usegalaxy.org/published/workflow?id=f39603063febba82, https://usegalaxy.org/published/workflow?id=f47f0b25c1405128, https://usegalaxy.org/published/workflow?id=f58970e6914a1bba, https://usegalaxy.org/published/workflow?id=f857e8282af234e0, https://usegalaxy.org/published/workflow?id=f895ed9fb68d3379, https://usegalaxy.org/published/workflow?id=fe2d15d352a9919f, https://usegalaxy.org/published/workflow?id=fe3d4001499c3f15, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86, https://workflowhub.eu/workflows/655?version=1 ecology/ENA_Biodiv_submission, ecology/Obitools-metabarcoding, sequence-analysis/Manage_AB1_Sanger
fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 201 274 2312 3149 730 2149 5368 14632 105 160 4058 4894 13 13 163 163 1049 4694 11901 46640 https://dev.workflowhub.eu/workflows/1281?version=1, https://usegalaxy.eu/published/workflow?id=7734928ebc0a2654, https://usegalaxy.org.au/published/workflow?id=5926a7669eabb1c6, https://usegalaxy.org/published/workflow?id=41b181f1d763e419, https://usegalaxy.org/published/workflow?id=86838846a266181d transcriptomics/srna
fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 51 53 232 263 263 990 2140 8239 11 18 387 508 7 7 22 22 332 1732 2781 14594 https://usegalaxy.org/published/workflow?id=958f78270fc8f55c, https://usegalaxy.org/published/workflow?id=aef91b21e3b72f70 sequence-analysis/Manage_AB1_Sanger
fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 532 695 6299 9698 1873 2507 14303 20805 226 267 2337 2864 52 52 498 498 2683 8887 23437 80739 https://usegalaxy.org/published/workflow?id=ae81cc0e8263d03e, https://usegalaxy.org/published/workflow?id=b1b75a9323d25085, https://usegalaxy.org/published/workflow?id=c2c6779a8b1821e0
fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2554 2763 19286 21211 3824 4313 24257 27546 1452 1501 6500 6992 84 84 818 818 7914 24489 50861 158289 https://dev.workflowhub.eu/workflows/1003?version=1, https://dev.workflowhub.eu/workflows/1092?version=1, https://dev.workflowhub.eu/workflows/1192?version=2, https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=56edd22d14392691, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=95cb04ffb473623b, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=b7c2440621968526, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=f6e8a63283262518, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.org.au/published/workflow?id=408a31694e9c85e6, https://usegalaxy.org.au/published/workflow?id=874492eb776ba813, https://usegalaxy.org.au/published/workflow?id=9b75924c483b5f6b, https://usegalaxy.org.au/published/workflow?id=aee5b5645c51cac3, https://usegalaxy.org.au/published/workflow?id=fb0986a952c35e0a, https://usegalaxy.org/published/workflow?id=0a57740c68e85e21, https://usegalaxy.org/published/workflow?id=4e1ae78405034ad3, https://usegalaxy.org/published/workflow?id=51c485af11d90700, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=c30f6ca171896908, https://usegalaxy.org/published/workflow?id=c446105e87750aa2, https://usegalaxy.org/published/workflow?id=e745c45651d829b8, https://usegalaxy.org/published/workflow?id=f926e70bee242785, https://workflowhub.eu/workflows/365?version=1 assembly/general-introduction, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short
fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 558 723 16132 17870 1864 5836 23649 59636 178 224 1758 2357 22 22 182 182 2622 12049 41721 163487 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=bab0322cc0346d81, https://usegalaxy.org/published/workflow?id=5df593510c7d944d, https://usegalaxy.org/published/workflow?id=8d3557a82f49528c, https://usegalaxy.org/published/workflow?id=c337e5265a8079d0, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22
fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 481 575 3999 4420 1362 3512 28121 40003 217 249 810 1055 9 9 14 14 2069 8483 32944 111380 https://usegalaxy.org/published/workflow?id=f823b87dd06ba4ac
fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Graphics, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 131 188 1218 1409 1987 9047 12098 60002 32 58 203 510 13 13 89 89 2163 13632 13608 89226 https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3c32ad1a07a66843, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=6ad3c2d8a14809ca, https://usegalaxy.org/published/workflow?id=8ea5aaa1cc088077, https://usegalaxy.org/published/workflow?id=b7e20495b47d5b97, https://usegalaxy.org/published/workflow?id=c29b08d56223c274, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a
fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 46 51 320 359 258 2243 1370 9719 12 27 1146 1374 4 4 21 21 320 2965 2857 17187 https://usegalaxy.org/published/workflow?id=3767c9c07462b777
fastq_quality_filter cshl_fastq_quality_filter Filter by quality 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 4153 4545 34267 36002 6088 13148 48714 140725 1878 2211 8194 10285 221 221 982 982 12340 44805 92157 372308 https://dev.workflowhub.eu/workflows/1094?version=1, https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=055eae88be2d4dd7, https://usegalaxy.eu/published/workflow?id=13da0b6780007d12, https://usegalaxy.eu/published/workflow?id=1502fd3fa90d32d8, https://usegalaxy.eu/published/workflow?id=1d0f438faa441c4e, https://usegalaxy.eu/published/workflow?id=2a274e0e4ba45c77, https://usegalaxy.eu/published/workflow?id=2aac571c44e6a7c8, https://usegalaxy.eu/published/workflow?id=38c7fa2653c5a2ee, https://usegalaxy.eu/published/workflow?id=39bf638cd7b56fd6, https://usegalaxy.eu/published/workflow?id=4c736e255f4a740f, https://usegalaxy.eu/published/workflow?id=63749bd3045ccd4a, https://usegalaxy.eu/published/workflow?id=71cac07a151f9470, https://usegalaxy.eu/published/workflow?id=76a63b1710da5e60, https://usegalaxy.eu/published/workflow?id=9a1d17c12b139bda, https://usegalaxy.eu/published/workflow?id=a8d814a6d86e9661, https://usegalaxy.eu/published/workflow?id=bd74a116e3f8d5b8, https://usegalaxy.eu/published/workflow?id=c65d98740ca64104, https://usegalaxy.eu/published/workflow?id=ccec1752fcac5e3f, https://usegalaxy.eu/published/workflow?id=d3ae8c51061330f3, https://usegalaxy.eu/published/workflow?id=d5780c37232e3181, https://usegalaxy.eu/published/workflow?id=da3a6d229e422dde, https://usegalaxy.eu/published/workflow?id=db63d53712d2571b, https://usegalaxy.eu/published/workflow?id=dbcf7af09e036754, https://usegalaxy.eu/published/workflow?id=e47351e2edd93a1a, https://usegalaxy.eu/published/workflow?id=e6c5fb1d37d29ec0, https://usegalaxy.eu/published/workflow?id=e85c9385870aadcc, https://usegalaxy.eu/published/workflow?id=f0209559f3686fcc, https://usegalaxy.eu/published/workflow?id=f81534f6cf8733e7, https://usegalaxy.org.au/published/workflow?id=0ed947e76a69028b, https://usegalaxy.org.au/published/workflow?id=5a0fc3b91ae47788, https://usegalaxy.org.au/published/workflow?id=acaca80c4a0c76c8, https://usegalaxy.org.au/published/workflow?id=b46bc04e0418fdfa, https://usegalaxy.org.au/published/workflow?id=c622bd03677314aa, https://usegalaxy.org/published/workflow?id=02d49c5f0d9aa010, https://usegalaxy.org/published/workflow?id=0555313573cd1ee2, https://usegalaxy.org/published/workflow?id=08edef22fa132799, https://usegalaxy.org/published/workflow?id=0d6a4dfbccafd2a2, https://usegalaxy.org/published/workflow?id=0f43fdfe1824e9d7, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=26b2057a8bc0386c, https://usegalaxy.org/published/workflow?id=3e6d4ab34de7918c, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=58a7a02dade085cf, https://usegalaxy.org/published/workflow?id=58a91a914e381dcf, https://usegalaxy.org/published/workflow?id=58ceaed0a42fe60a, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=6c49d9c25ba4ddf5, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=8356ee639055cbca, https://usegalaxy.org/published/workflow?id=947340358dd268ea, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://usegalaxy.org/published/workflow?id=b6c0208e49cd2271, https://usegalaxy.org/published/workflow?id=cd3bce36b6ef073d, https://usegalaxy.org/published/workflow?id=d8afd017905d6702 introduction/galaxy-intro-short
fastq_stats fastq_stats FASTQ Summary Statistics by column 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 666 866 3760 4783 2843 14363 13952 82654 144 265 3781 4275 49 49 282 282 3702 22947 21775 135544 https://usegalaxy.eu/published/workflow?id=6d3ec4203b503810, https://usegalaxy.eu/published/workflow?id=e299721eec23b557, https://usegalaxy.org/published/workflow?id=0017c434354b6f6a, https://usegalaxy.org/published/workflow?id=055eb85c8ecf0ca3, https://usegalaxy.org/published/workflow?id=165c8a58baffe64c, https://usegalaxy.org/published/workflow?id=24adb067c82862fa, https://usegalaxy.org/published/workflow?id=2b3970d9b28810a1, https://usegalaxy.org/published/workflow?id=4339d5625c15ae78, https://usegalaxy.org/published/workflow?id=684ff8ee49c7f116, https://usegalaxy.org/published/workflow?id=6f436066dffbc37d, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=ab23c641cfdefe0c, https://usegalaxy.org/published/workflow?id=b4dda054d2cf15b7, https://usegalaxy.org/published/workflow?id=b72edafe11293d93, https://usegalaxy.org/published/workflow?id=dcb73fce390b36b2, https://usegalaxy.org/published/workflow?id=e2fa6584853a0dee, https://usegalaxy.org/published/workflow?id=e35ac40c58953f74, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=f201ce61becf9a80, https://usegalaxy.org/published/workflow?id=f3983646b6df24bf
fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Convert Formats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 1444 1549 42408 46165 2846 6719 45571 104394 454 694 9657 15445 168 168 2963 2963 4912 18954 100599 370165 https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358 ecology/eDNA-taxonomic-analysis, sequence-analysis/Manage_AB1_Sanger
fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 289 329 15714 17127 620 1864 13207 32110 65 93 6138 6473 24 24 2027 2027 998 4306 37086 131909 https://dev.workflowhub.eu/workflows/1287?version=2, https://dev.workflowhub.eu/workflows/1292?version=2, https://dev.workflowhub.eu/workflows/1307?version=1, https://usegalaxy.eu/published/workflow?id=4643edf74f3eaec3, https://usegalaxy.eu/published/workflow?id=5e1b048040ea7535, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=acb9131e84de1ae0, https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=79ca45e45d76871f, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=1e1a299825f27f11, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=5de035c08af915ea, https://usegalaxy.org/published/workflow?id=86838846a266181d, https://usegalaxy.org/published/workflow?id=b6c0208e49cd2271, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9 contributing/create-new-tutorial, sequence-analysis/Manage_AB1_Sanger, single-cell/scrna-data-ingest
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fastqc fastqc Read QC reports using FastQC 2017-01-11 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 0.74+galaxy1 fastqc 0.12.1 To update Fastq Manipulation Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis Sequencing, Data quality management, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. 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fastqe fastqe FASTQE 2020-07-13 https://fastqe.com/ 0.3.1+galaxy0 fastqe 0.3.3 To update Sequence Analysis Sequencing quality control Sequencing quality control Sequence analysis, Sequencing Sequence analysis, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2748 2748 5999 5999 5370 5370 11770 11770 1047 1047 2786 2786 268 268 453 453 9433 28299 21008 63024 https://usegalaxy.eu/published/workflow?id=055eae88be2d4dd7, https://usegalaxy.eu/published/workflow?id=2a274e0e4ba45c77, https://usegalaxy.eu/published/workflow?id=340aa3ae5468deb0, https://usegalaxy.eu/published/workflow?id=4c736e255f4a740f, https://usegalaxy.eu/published/workflow?id=519e0ffdfd1790bc, https://usegalaxy.eu/published/workflow?id=76a63b1710da5e60, https://usegalaxy.eu/published/workflow?id=a8d814a6d86e9661, https://usegalaxy.eu/published/workflow?id=c65d98740ca64104, https://usegalaxy.eu/published/workflow?id=d3ae8c51061330f3, https://usegalaxy.eu/published/workflow?id=d5780c37232e3181, https://usegalaxy.org.au/published/workflow?id=115151c2c8998d44, https://usegalaxy.org.au/published/workflow?id=178db14511c8f293, https://usegalaxy.org.au/published/workflow?id=1f63ec596e578b1c, https://usegalaxy.org.au/published/workflow?id=43f2dabbc1932e30, https://usegalaxy.org.au/published/workflow?id=47cacc06d404a8c6, https://usegalaxy.org.au/published/workflow?id=5d6773ed5b2f41cb, https://usegalaxy.org.au/published/workflow?id=8fe84de499e96485, https://usegalaxy.org.au/published/workflow?id=bd251174d94cde9d, https://usegalaxy.org.au/published/workflow?id=dd6f465ab1eb10b0, https://usegalaxy.org.au/published/workflow?id=e08b04291839e79a, https://usegalaxy.org/published/workflow?id=20da2dcce0ae2ca2, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=cf2dbc29ca20ebee, https://usegalaxy.org/published/workflow?id=fe262214fba1cb8e sequence-analysis/quality-control
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fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL 2018-02-02 http://www.microbesonline.org/fasttree/ 2.1.10 fasttree 2.1.11 To update Phylogenetics Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 1355 1398 72006 72254 2526 2527 28673 28676 700 815 7608 8265 45 45 304 304 4626 14037 108591 326681 https://dev.workflowhub.eu/workflows/1077?version=2, https://dev.workflowhub.eu/workflows/1296?version=2, https://dev.workflowhub.eu/workflows/40?version=1, https://dev.workflowhub.eu/workflows/43?version=1, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=ce21961260fe4351, https://usegalaxy.eu/published/workflow?id=d07fe8b5a045c176, https://usegalaxy.eu/published/workflow?id=dc57118a95b10a80, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.fr/published/workflow?id=c7be6e229a045fad, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=d62b6717202f42c9, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=87685c6247521b54, https://usegalaxy.org/published/workflow?id=be54e57345ce7ca5, https://usegalaxy.org/published/workflow?id=be9bd7286d38c210, https://workflowhub.eu/workflows/1060?version=1 evolution/abc_intro_phylo, evolution/bacterial-comparative-genomics, microbiome/pathogen-detection-from-nanopore-foodborne-data
fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 81 110 1763 2321 313 2445 5740 25714 29 52 665 1136 3 3 4 4 426 3462 8172 45519 https://usegalaxy.org/published/workflow?id=02c9244e2fb060de, https://usegalaxy.org/published/workflow?id=02d49c5f0d9aa010, https://usegalaxy.org/published/workflow?id=8356ee639055cbca, https://usegalaxy.org/published/workflow?id=947340358dd268ea, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f, https://usegalaxy.org/published/workflow?id=fe3d4001499c3f15
fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 228 272 21410 23181 917 2823 44990 99937 56 73 922 1104 16 16 47 47 1217 5618 67369 259007 https://usegalaxy.org/published/workflow?id=87b6bac79f99c1f8, https://usegalaxy.org/published/workflow?id=cd431e5f912d3616
fastx_clipper cshl_fastx_clipper Clip adapter sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 235 275 3477 3882 1159 6149 12928 118973 37 59 438 770 5 5 10 10 1436 9360 16853 157341 https://usegalaxy.org/published/workflow?id=02c9244e2fb060de, https://usegalaxy.org/published/workflow?id=29a80db9f3208c29, https://usegalaxy.org/published/workflow?id=344a79d4f12d2cff, https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=77e4bb9d6aea0c9a, https://usegalaxy.org/published/workflow?id=85c3a1fc1d3d3df8, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=b0a12221ce09c001, https://usegalaxy.org/published/workflow?id=b2176abeb937f026, https://usegalaxy.org/published/workflow?id=c64719e91e7346a2, https://usegalaxy.org/published/workflow?id=cd14df23bb05db2c, https://usegalaxy.org/published/workflow?id=d69ea491b99016f4, https://usegalaxy.org/published/workflow?id=d860749fd34809d7, https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f, https://usegalaxy.org/published/workflow?id=d8afd017905d6702, https://usegalaxy.org/published/workflow?id=e6838c861b6beaed, https://usegalaxy.org/published/workflow?id=fe3d4001499c3f15
fastx_collapser cshl_fastx_collapser Collapse sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 340 381 69364 81050 821 3165 77689 193356 59 83 23148 23755 41 42 218 228 1261 6193 170419 639227 https://usegalaxy.org/published/workflow?id=091896754bcc8ec1, https://usegalaxy.org/published/workflow?id=1708fdfd1d485434, https://usegalaxy.org/published/workflow?id=1a6f552cfe798883, https://usegalaxy.org/published/workflow?id=23bca854e549ad48, https://usegalaxy.org/published/workflow?id=2823322fa85c7ae1, https://usegalaxy.org/published/workflow?id=2d1d69aac67a387a, https://usegalaxy.org/published/workflow?id=2e92cca68b7979f6, https://usegalaxy.org/published/workflow?id=49ca77212cc56ef9, https://usegalaxy.org/published/workflow?id=52cc435f50a6ff29, https://usegalaxy.org/published/workflow?id=52e099f693639115, https://usegalaxy.org/published/workflow?id=5e079a9ac49a5b8c, https://usegalaxy.org/published/workflow?id=66bc5f6d71466b7f, https://usegalaxy.org/published/workflow?id=74fe080f24f7da84, https://usegalaxy.org/published/workflow?id=80afe572b6693ca1, https://usegalaxy.org/published/workflow?id=86838846a266181d, https://usegalaxy.org/published/workflow?id=98286b6154e1b57f, https://usegalaxy.org/published/workflow?id=9efb061a87bc9f4d, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=bb8609e8d2d4bd89, https://usegalaxy.org/published/workflow?id=c74a01ba2f2a80d3, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22
fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Graphics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 55 93 156 274 1126 4338 4355 25604 72 98 1076 1214 9 9 11 11 1262 7062 5598 38299 https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3c32ad1a07a66843, https://usegalaxy.org/published/workflow?id=8ea5aaa1cc088077, https://usegalaxy.org/published/workflow?id=b7e20495b47d5b97, https://usegalaxy.org/published/workflow?id=c29b08d56223c274
fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 158 214 2192 2360 4015 10466 23935 65308 251 288 2823 3288 5 5 65 65 4429 19831 29015 129051 https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3c32ad1a07a66843, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=6ad3c2d8a14809ca, https://usegalaxy.org/published/workflow?id=8ea5aaa1cc088077, https://usegalaxy.org/published/workflow?id=b7e20495b47d5b97, https://usegalaxy.org/published/workflow?id=c29b08d56223c274
fastx_renamer cshl_fastx_renamer Rename sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 195 236 3328 3708 289 1045 9173 14497 51 69 495 787 11 11 629 629 546 2453 13625 46871 https://usegalaxy.eu/published/workflow?id=08cfb9b21c1ec808, https://usegalaxy.eu/published/workflow?id=d4b3da4cc5a50044, https://usegalaxy.org/published/workflow?id=1a6f552cfe798883, https://usegalaxy.org/published/workflow?id=23bca854e549ad48, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=2823322fa85c7ae1, https://usegalaxy.org/published/workflow?id=2d1d69aac67a387a, https://usegalaxy.org/published/workflow?id=2e92cca68b7979f6, https://usegalaxy.org/published/workflow?id=49ca77212cc56ef9, https://usegalaxy.org/published/workflow?id=52cc435f50a6ff29, https://usegalaxy.org/published/workflow?id=52e099f693639115, https://usegalaxy.org/published/workflow?id=5e079a9ac49a5b8c, https://usegalaxy.org/published/workflow?id=66bc5f6d71466b7f, https://usegalaxy.org/published/workflow?id=74fe080f24f7da84, https://usegalaxy.org/published/workflow?id=80afe572b6693ca1, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=bb8609e8d2d4bd89, https://usegalaxy.org/published/workflow?id=c74a01ba2f2a80d3
fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 381 457 11861 14038 588 1596 18069 68766 70 89 738 928 18 18 3514 3514 1057 4274 34182 155610 https://dev.workflowhub.eu/workflows/1287?version=2, https://dev.workflowhub.eu/workflows/1292?version=2, https://usegalaxy.eu/published/workflow?id=6d3ec4203b503810, https://usegalaxy.eu/published/workflow?id=e299721eec23b557, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=58a7a02dade085cf, https://usegalaxy.org/published/workflow?id=86838846a266181d, https://usegalaxy.org/published/workflow?id=b18a41e364650fee sequence-analysis/Manage_AB1_Sanger
fastx_trimmer cshl_fastx_trimmer Trim sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 579 709 13907 15425 1830 8459 125452 213856 224 279 3212 5400 252 252 1645 1645 2885 15469 144216 524758 https://usegalaxy.eu/published/workflow?id=4643edf74f3eaec3, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=987a2abb5cd56e57, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.org/published/workflow?id=5641d1cbe795203f, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=b2176abeb937f026, https://usegalaxy.org/published/workflow?id=e6838c861b6beaed, https://usegalaxy.org/published/workflow?id=e7030b62a3335bd7
featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome 2016-02-09 https://subread.sourceforge.net/ 2.1.1 subread 2.1.1 Up-to-date RNA, Transcriptomics, Sequence Analysis Read summarisation, RNA-Seq quantification Read summarisation, RNA-Seq quantification RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 12867 14177 778663 819416 24978 30432 698749 877978 2478 2679 71903 75982 1332 1332 33406 33407 41655 131930 1582721 4972225 https://dev.workflowhub.eu/workflows/1001?version=1, https://dev.workflowhub.eu/workflows/1214?version=1, https://dev.workflowhub.eu/workflows/1295?version=1, https://dev.workflowhub.eu/workflows/1319?version=2, https://dev.workflowhub.eu/workflows/1327?version=1, https://dev.workflowhub.eu/workflows/1329?version=5, https://usegalaxy.eu/published/workflow?id=0229f3f3835c2d53, https://usegalaxy.eu/published/workflow?id=08cfb9b21c1ec808, https://usegalaxy.eu/published/workflow?id=0de150b19102cb7e, https://usegalaxy.eu/published/workflow?id=135e8888872e8413, https://usegalaxy.eu/published/workflow?id=1502fd3fa90d32d8, https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, 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feelnc feelnc Galaxy wrapper for FEELnc 2018-03-27 https://github.com/tderrien/FEELnc 0.2.1 feelnc 0.2 To update Sequence Analysis Annotation, Classification Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 117 124 1461 1616 129 129 1116 1116 5 5 81 81 14 14 68 68 265 802 2726 8333 https://dev.workflowhub.eu/workflows/1141?version=1, https://usegalaxy.eu/published/workflow?id=93e576fca98a554d genome-annotation/lncrna
fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. 2017-01-05 https://github.com/lh3/fermikit r193 fermi2 r193 Up-to-date Assembly, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fgsea fgsea Perform gene set testing using fgsea 2018-10-19 https://bioconductor.org/packages/release/bioc/html/fgsea.html 1.8.0+galaxy1 bioconductor-fgsea 1.32.2 To update Visualization, Transcriptomics, Statistics, Single Cell Gene-set enrichment analysis Gene-set enrichment analysis Genetics Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 603 672 6428 7619 1032 1032 22800 22805 117 121 945 970 8 8 74 74 1760 5353 30247 91962 https://dev.workflowhub.eu/workflows/1316?version=1, https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=73a9ab4f0f0b9907, https://usegalaxy.eu/published/workflow?id=9a83043d5e847318, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3, https://usegalaxy.org/published/workflow?id=68832752b883c226 transcriptomics/rna-seq-genes-to-pathways
filtlong filtlong Filtlong - Filtering long reads by quality 2018-09-14 https://github.com/rrwick/Filtlong 0.2.1 filtlong 0.2.1 Up-to-date Fastq Manipulation, Sequence Analysis Filtering, Sequencing quality control Filtering, Sequencing quality control iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1727 1822 64393 65388 1012 1012 34007 34008 657 657 11502 11502 19 19 106 106 3415 10340 110008 331020 https://dev.workflowhub.eu/workflows/1178?version=1, https://usegalaxy.eu/published/workflow?id=201e65bcf2b71584, https://usegalaxy.eu/published/workflow?id=346b46e6316c6950, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c3bfedf33bb00069, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=b7aa22291322e505, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=d69a765cfc82a399, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://workflowhub.eu/workflows/51?version=1 assembly/mrsa-nanopore
flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. 2020-11-06 https://github.com/BrooksLabUCSC/flair 1.5 flair 2.2.0 To update Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 49 49 2009 2009 0 0 0 0 0 0 0 0 0 0 0 0 49 147 2009 6027 https://usegalaxy.eu/published/workflow?id=d4a6fb334f5dd10e
flash flash Fast Length Adjustment of SHort reads 2017-09-25 https://ccb.jhu.edu/software/FLASH/ 1.2.11 flash 1.2.11 Up-to-date Assembly, Fastq Manipulation Read pre-processing, Sequence merging, Sequence assembly Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 239 277 27283 27740 435 727 9297 15450 1 1 4 4 0 0 0 0 675 2355 36584 116362 https://usegalaxy.eu/published/workflow?id=4643edf74f3eaec3, https://usegalaxy.eu/published/workflow?id=987a2abb5cd56e57, https://workflowhub.eu/workflows/100?version=1
fraggenescan fraggenescan Tool for finding (fragmented) genes in short read 2017-09-04 https://sourceforge.net/projects/fraggenescan/ fraggenescan 1.32 To update Sequence Analysis Gene prediction Gene prediction Genetics, Sequence analysis Genetics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 148 170 1242 1543 0 0 0 0 47 47 1117 1117 2 2 11 11 197 613 2370 7411 https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=534f5fc25bc887ca, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=d57d41e306241396
freebayes freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool 2017-01-11 https://github.com/ekg/freebayes 1.3.9 freebayes 1.3.10 To update Variant Analysis Variant calling, Statistical calculation Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases Genomics, Genetic variation, Rare diseases devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 2 2 2 0 8990 9881 160042 184007 16349 26957 147934 268340 2322 2770 20735 24354 323 323 2784 2784 27984 95899 331495 1142475 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https://usegalaxy.org/published/workflow?id=f302d673420a9bdd, https://usegalaxy.org/published/workflow?id=f39603063febba82, https://usegalaxy.org/published/workflow?id=f3ed710e251833a7, https://usegalaxy.org/published/workflow?id=f4ed1c9434ed0445, https://usegalaxy.org/published/workflow?id=f60818a405f1bbbd, https://usegalaxy.org/published/workflow?id=f63f7a0a33a83841, https://usegalaxy.org/published/workflow?id=f88f186bc851e954, https://usegalaxy.org/published/workflow?id=f9d546aae406cf15, https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72, https://usegalaxy.org/published/workflow?id=feeec17310351914, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86, https://workflowhub.eu/workflows/111?version=5, https://workflowhub.eu/workflows/628?version=1, https://workflowhub.eu/workflows/676?version=1 proteomics/neoantigen-2-non-reference-database-generation, proteomics/proteogenomics-dbcreation, variant-analysis/dip, variant-analysis/dunovo, variant-analysis/exome-seq, variant-analysis/non-dip, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants
freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation 2022-07-05 https://github.com/andersen-lab/Freyja 1.5.2 freyja 1.5.3 To update Metagenomics, Sequence Analysis RNA-Seq quantification RNA-Seq quantification Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 114 114 24563 24563 27 27 283 283 0 0 0 0 0 0 0 0 141 423 24846 74538 https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b
funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. 2021-08-26 https://funannotate.readthedocs.io 1.8.17 To update Genome annotation Genome annotation Genome annotation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 1741 1741 11102 11102 79 79 360 360 661 661 7353 7353 246 246 1401 1401 2727 8181 20216 60648 https://dev.workflowhub.eu/workflows/1202?version=1, https://dev.workflowhub.eu/workflows/1264?version=2, https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://usegalaxy.org.au/published/workflow?id=52065a4100b11184, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/754?version=1 ecology/phylogeny-data-prep, genome-annotation/funannotate
gatk4_mutect2 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK 2019-10-28 https://software.broadinstitute.org/gatk/gatk4 4.1.7.0 gatk4 4.6.2.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 502 512 3722 3797 1777 1778 10032 10036 0 0 0 0 0 0 0 0 2279 6848 13754 41341 https://usegalaxy.eu/published/workflow?id=93e32219d412c1f1, https://usegalaxy.eu/published/workflow?id=b02d90c32dc67730, https://usegalaxy.org/published/workflow?id=39753cc73284963f, https://usegalaxy.org/published/workflow?id=eb33df15225b8aa0, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://workflowhub.eu/workflows/35?version=1
gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format 2017-06-23 http://bioinf.iasi.cnr.it/gdcwebapp/ 1.0.0 python To update Data Source, Convert Formats iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gecko gecko Ungapped genome comparison 2020-11-25 https://github.com/otorreno/gecko 1.2 gecko 1.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 285 285 879 879 0 0 0 0 120 120 874 874 0 0 0 0 405 1215 1753 5259 https://dev.workflowhub.eu/workflows/1160?version=2 genome-annotation/hpc-for-lsgc
gem_tools gem_check_memote, gem_escher_visualization, gem_extract_exchange, gem_flux_distribution, gem_flux_variability_analysis, gem_knockout, gem_phenotype_phase_plane Tools for analyzing genome-scale metabolic models (GEMs) using COBRApy and related libraries. 2024-12-01 https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology 0.29.1 cobra 0.21.0 To update Metabolomics, Systems Biology, Synthetic Biology iuc https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology https://github.com/galaxyproject/tools-iuc/tree/main/tools/gem_tools 0 7 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gemini glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. 2017-11-28 https://ccb.jhu.edu/software/glimmer/ 3.02 glimmer 3.02 Up-to-date Sequence Analysis Sequence analysis, Genetic variation analysis Sequence analysis, Genetic variation analysis Sequence analysis Sequence analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 470 470 4543 4543 0 0 0 0 0 0 0 0 0 0 0 0 470 1410 4543 13629 https://dev.workflowhub.eu/workflows/1264?version=2, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178, https://workflowhub.eu/workflows/358?version=1 ecology/phylogeny-data-prep
gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation 2014-11-09 https://github.com/arq5x/gemini 0.20.1 gemini 0.30.2 To update Sequence Analysis, Next Gen Mappers Sequence analysis, Genetic variation analysis Sequence analysis, Genetic variation analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1868 2080 4844 5696 441 532 1502 1628 485 488 4039 4175 41 41 78 78 2835 8811 10463 32503 https://dev.workflowhub.eu/workflows/1096?version=2, https://dev.workflowhub.eu/workflows/1104?version=1, https://dev.workflowhub.eu/workflows/1108?version=1, https://dev.workflowhub.eu/workflows/1114?version=1, https://usegalaxy.eu/published/workflow?id=2aede5c6577b28f5, https://usegalaxy.eu/published/workflow?id=3570835f21365be7, https://usegalaxy.eu/published/workflow?id=b3b094f1bdbaa04a, https://usegalaxy.eu/published/workflow?id=b3c0eba755f269b2, https://usegalaxy.eu/published/workflow?id=b82a4065be048ef6, https://usegalaxy.org.au/published/workflow?id=1be22b394f9ec3ab, https://usegalaxy.org.au/published/workflow?id=5442f0437ade82c4, https://usegalaxy.org.au/published/workflow?id=ac89c2d51c32cc9c, https://workflowhub.eu/workflows/363?version=2 variant-analysis/dip, variant-analysis/exome-seq, variant-analysis/trio-analysis
genebed_maf_to_fasta GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals 2020-08-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ 1.0.1+galaxy0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1 1 1 1 0 1 0 0 0 1 1 0 0 0 1 1 1 0 1 0 0 0 0 1 1 0 0 0 1 1 1 1 1 0 2 2 4 4 19 279 210 2905 0 0 0 0 0 0 0 0 21 323 214 3337
genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility 2017-11-27 https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 3.0.0 ghm 3.1 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
geneiobio gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. 2023-06-20 https://github.com/iobio/gene.iobio 4.7.1+galaxy1 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 143 143 0 0 0 0 7 7 102 102 0 0 0 0 43 129 245 735 https://dev.workflowhub.eu/workflows/1096?version=2, https://usegalaxy.eu/published/workflow?id=b3c0eba755f269b2 variant-analysis/trio-analysis
genetrack genetrack Contains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand. 2015-12-18 numpy To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 201 365 670 0 0 0 0 0 0 0 0 94 389 365 1400
genomescope genomescope Analyze unassembled short reads 2021-04-30 https://github.com/tbenavi1/genomescope2.0 2.0.1 genomescope2 2.0.1 Up-to-date Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 746 746 3589 3589 514 514 2506 2506 167 167 1857 1857 31 31 588 588 1458 4374 8540 25620 https://dev.workflowhub.eu/workflows/1002?version=1, https://dev.workflowhub.eu/workflows/1127?version=3, https://dev.workflowhub.eu/workflows/1166?version=2, https://dev.workflowhub.eu/workflows/1187?version=2, https://usegalaxy.eu/published/workflow?id=0e642b5407dd595b, https://usegalaxy.eu/published/workflow?id=0fef06a87389eb59, https://usegalaxy.eu/published/workflow?id=11ce7a7bf3d075e0, https://usegalaxy.eu/published/workflow?id=238606356787b876, https://usegalaxy.eu/published/workflow?id=29b4710cd24995b2, https://usegalaxy.eu/published/workflow?id=3069c17b52decab4, https://usegalaxy.eu/published/workflow?id=3788bb24b97f7b83, https://usegalaxy.eu/published/workflow?id=7f5da1ebd6673841, https://usegalaxy.eu/published/workflow?id=a85be448600a6789, https://usegalaxy.eu/published/workflow?id=acd29212884f967b, https://usegalaxy.eu/published/workflow?id=acfc7d1b03d5fbd0, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=c2c7f1815c411bfb, https://usegalaxy.eu/published/workflow?id=d1e3d3bb0922d771, https://usegalaxy.eu/published/workflow?id=d67299c34e63f3d9, https://usegalaxy.eu/published/workflow?id=db6640887b5ca0cd, https://usegalaxy.eu/published/workflow?id=dec16871152fac35, https://usegalaxy.eu/published/workflow?id=ff16623a63ff5124, https://usegalaxy.org.au/published/workflow?id=049f61f436ff66df, https://usegalaxy.org.au/published/workflow?id=141ac7a106e49d8f, https://usegalaxy.org.au/published/workflow?id=26b57e0b79ea4559, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=5364e6ec5b4f48cd, https://usegalaxy.org.au/published/workflow?id=6aaaa084d5339c08, https://usegalaxy.org.au/published/workflow?id=6c54e7f7a4bf17ed, https://usegalaxy.org.au/published/workflow?id=6c5b84bcac127272, https://usegalaxy.org.au/published/workflow?id=8dc05e3ba64e981f, https://usegalaxy.org.au/published/workflow?id=ab9f7a97baaa7fa6, https://usegalaxy.org.au/published/workflow?id=b9d0a39d72b8e5f8, https://usegalaxy.org.au/published/workflow?id=c0aa1f64a89a6115, https://usegalaxy.org.au/published/workflow?id=d7c2d0d49b1a6c86, https://usegalaxy.org.au/published/workflow?id=d9ee934bbae0fa01, https://usegalaxy.org/published/workflow?id=14dc039ee7138b8b, https://usegalaxy.org/published/workflow?id=19e2191687f81c21, https://usegalaxy.org/published/workflow?id=2759eaa8adbd2857, https://usegalaxy.org/published/workflow?id=333c5725006e4154, https://usegalaxy.org/published/workflow?id=49e2570e363fda11, https://usegalaxy.org/published/workflow?id=5503f7835226bc04, https://usegalaxy.org/published/workflow?id=7f8d7595cbeebf1d, https://usegalaxy.org/published/workflow?id=815cd221eaaaeb53, https://usegalaxy.org/published/workflow?id=83898f7cbfb7f88e, https://usegalaxy.org/published/workflow?id=9bc46b4d35749b41, https://usegalaxy.org/published/workflow?id=a00f78b74c27b5f3, https://usegalaxy.org/published/workflow?id=ae71399852f34680, https://usegalaxy.org/published/workflow?id=bcf3ff03326c80b7, https://usegalaxy.org/published/workflow?id=c72f94a30ad54327, https://usegalaxy.org/published/workflow?id=faa4f94f070c6213, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/223?version=1, https://workflowhub.eu/workflows/365?version=1, https://workflowhub.eu/workflows/366?version=1, https://workflowhub.eu/workflows/603?version=2, https://workflowhub.eu/workflows/631?version=5, https://workflowhub.eu/workflows/632?version=8, https://workflowhub.eu/workflows/698?version=1 assembly/ERGA-post-assembly-QC, assembly/largegenome, assembly/vgp_genome_assembly
genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases 2022-01-12 https://github.com/shbrief/GenomicSuperSignature 1.2.0 bioconductor-genomicsupersignature 1.14.0 To update Sequence Analysis, RNA, Transcriptomics Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17 17 55 55 0 0 0 0 0 0 0 0 0 0 0 0 17 51 55 165
genrich genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). 2019-07-05 https://github.com/jsh58/Genrich 0.5+galaxy2 genrich 0.6.1 To update ChIP-seq iuc https://github.com/jsh58/Genrich https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 364 420 2867 3663 445 445 2965 2965 31 31 628 628 0 0 0 0 840 2576 6460 20176 https://usegalaxy.eu/published/workflow?id=02655d0e4af0ee0d, https://usegalaxy.org.au/published/workflow?id=99821674db7682bb
geopandas geopandas_table2geojson GeoPandas is an open source project to make working with geospatial data easier. 2025-04-20 https://geopandas.org 1.0.1 geopandas To update Geo Science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
get_hrun get_hrun Annotate indel variants with homopolymer context 2021-03-02 https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.4 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 9 9 0 0 0 0 0 0 0 0 0 0 0 0 5 15 9 27
getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. 2022-03-15 https://github.com/Kinggerm/GetOrganelle 1.7.7.1 getorganelle 1.7.7.1 Up-to-date Assembly De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 254 254 2735 2735 0 0 0 0 96 96 1088 1088 0 0 0 0 350 1050 3823 11469 https://usegalaxy.org.au/published/workflow?id=f2541030f6d70b59
gfa_to_fa gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format 2019-06-18 http://gfa-spec.github.io/GFA-spec/ 0.1.2 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 849 876 9989 10698 557 559 6441 6445 158 158 1282 1282 40 40 195 195 1604 4841 17907 54434 https://dev.workflowhub.eu/workflows/1002?version=1, https://dev.workflowhub.eu/workflows/1107?version=1, https://dev.workflowhub.eu/workflows/1187?version=2, https://dev.workflowhub.eu/workflows/584?version=1, https://dev.workflowhub.eu/workflows/585?version=1, https://dev.workflowhub.eu/workflows/586?version=1, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=d67299c34e63f3d9, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=fba1671d835b6dd3, https://usegalaxy.org.au/published/workflow?id=044b6b475b4db27a, https://usegalaxy.org.au/published/workflow?id=29f0c07c8a24b542, https://usegalaxy.org.au/published/workflow?id=36604d0ab0dee988, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=98d3def7da131b4c, https://usegalaxy.org.au/published/workflow?id=afab89bc468da8b3, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467, https://usegalaxy.org.au/published/workflow?id=f83a3cda33131fb8, https://workflowhub.eu/workflows/1162?version=1, https://workflowhub.eu/workflows/1163?version=1, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/221?version=3, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/605?version=1, https://workflowhub.eu/workflows/606?version=2, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/701?version=1, https://workflowhub.eu/workflows/702?version=1, https://workflowhub.eu/workflows/789?version=1 assembly/hifi-assembly, assembly/vgp_genome_assembly, microbiome/plasmid-metagenomics-nanopore
gff3_rebase gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) 2015-05-25 https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase 1.2 bcbiogff 0.6.6 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 77 1152 1173 44 44 206 206 12 12 152 152 1 1 1 1 132 398 1511 4554 https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6
gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. 2017-03-27 https://github.com/gpertea/gffcompare/ 0.12.9 gffcompare 0.12.9 Up-to-date Transcriptomics Sequence annotation Sequence annotation Nucleic acids, Sequence analysis Nucleic acids, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 993 1104 3718 4339 1767 2717 5188 8395 208 243 1543 1802 21 21 51 51 2989 10063 10500 35587 https://dev.workflowhub.eu/workflows/1042?version=1, https://dev.workflowhub.eu/workflows/1201?version=2, https://dev.workflowhub.eu/workflows/1319?version=2, https://dev.workflowhub.eu/workflows/1324?version=3, https://dev.workflowhub.eu/workflows/1386?version=1, https://dev.workflowhub.eu/workflows/1398?version=1, https://usegalaxy.eu/published/workflow?id=0de150b19102cb7e, https://usegalaxy.eu/published/workflow?id=2287afbf248d9c89, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.eu/published/workflow?id=e8202b7b6338005d, https://usegalaxy.eu/published/workflow?id=f026c4b8341ff94c, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=53010c2f1f207429, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org.au/published/workflow?id=e045a6064ad5fdc4, https://usegalaxy.org/published/workflow?id=4061e061f659449b, https://usegalaxy.org/published/workflow?id=454d7310d001a4d0, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=8700f593a3d642f5, https://usegalaxy.org/published/workflow?id=9c022f4028de0bc6, https://usegalaxy.org/published/workflow?id=e336bca259abd474 proteomics/neoantigen-2-non-reference-database-generation, proteomics/proteogenomics-dbcreation, transcriptomics/de-novo, transcriptomics/differential-isoform-expression
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ggupset emc-ggupset Create Upset Plots with ggupset 2022-12-17 https://github.com/const-ae/ggupset 1.0 r-ggupset To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. 2018-12-28 https://github.com/DanFaria/GOEnrichment 2.0.1 goenrichment 2.0.1 Up-to-date Genome annotation Gene-set enrichment analysis Gene-set enrichment analysis Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de CiĂŞncia. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 834 942 5785 6602 1229 1229 8548 8548 249 249 1494 1494 5 7 38 43 2317 7061 15865 48417 https://dev.workflowhub.eu/workflows/1315?version=1, https://dev.workflowhub.eu/workflows/1365?version=1, https://usegalaxy.eu/published/workflow?id=5f053303601cc630, https://usegalaxy.eu/published/workflow?id=7136ce9f18c74853, https://usegalaxy.org.au/published/workflow?id=d04b26372b28e8ed single-cell/GO-enrichment, transcriptomics/goenrichment
goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data 2016-11-12 https://bioconductor.org/packages/release/bioc/html/goseq.html 1.50.0 bioconductor-goseq 1.58.0 To update Statistics, RNA, Micro-array Analysis Gene functional annotation Gene functional annotation RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 2962 3455 21986 24488 3320 3686 26126 28741 623 623 4529 4529 90 90 743 743 6995 21844 53384 165269 https://dev.workflowhub.eu/workflows/1316?version=1, https://dev.workflowhub.eu/workflows/1326?version=3, https://dev.workflowhub.eu/workflows/1332?version=1, https://usegalaxy.eu/published/workflow?id=032ad839dab7ae70, https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=c1a6d11e1eab6a42, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.org.au/published/workflow?id=4f0814ec9f9f8425, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=420a332da24fb9e9, https://usegalaxy.org/published/workflow?id=742120336d5ff997, https://workflowhub.eu/workflows/1194?version=1, https://workflowhub.eu/workflows/689?version=1 transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways
gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more 2019-10-30 https://biit.cs.ut.ee/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 To update Statistics, Web Services iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 674 690 4173 4303 1321 1322 8156 8159 0 0 0 0 0 0 0 0 1995 6002 12329 37120 https://dev.workflowhub.eu/workflows/1365?version=1, https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414, https://usegalaxy.eu/published/workflow?id=5f053303601cc630, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org/published/workflow?id=092be3cf6e40282c, https://usegalaxy.org/published/workflow?id=68832752b883c226, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=dec0cf06fa059e65 single-cell/GO-enrichment
graphembed graphembed Compute a 2D embedding of a data matrix given supervised class information 2019-12-10 https://github.com/fabriziocosta/GraphEmbed 2.4 graph_embed 2.4 Up-to-date Statistics, Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6 6 70 78 47 47 129 130 0 0 0 0 0 0 0 0 53 159 199 606
graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees 2017-03-03 https://github.com/biobakery/graphlan graphlan 1.1.3 To update Metagenomics, Graphics, Phylogenetics Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics Metagenomics, Phylogenetics, Phylogenomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1378 1465 10837 12092 430 430 1575 1575 264 264 1250 1250 2 2 12 12 2074 6309 13674 42277 https://dev.workflowhub.eu/workflows/1088?version=1, https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf microbiome/metatranscriptomics, microbiome/metatranscriptomics-short
groot groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples 2024-05-14 https://github.com/will-rowe/groot 1.1.2 groot 1.1.2 Up-to-date Metagenomics Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Metagenomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 4 4 0 0 0 0 0 0 0 0 3 3 28 28 5 15 32 96
gtdb_to_taxdump gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format 2024-08-25 https://github.com/nick-youngblut/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Up-to-date Metagenomics Data handling, Mapping, Generation Data handling, Mapping, Generation Computational biology Computational biology iuc https://github.com/nick-youngblut/gtdb_to_taxdump https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 449 449 0 0 0 0 0 0 0 0 0 0 0 0 12 36 449 1347 https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1
gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 2022-12-13 https://github.com/Ecogenomics/GTDBTk 2.4.1 gtdbtk 2.4.1 Up-to-date Metagenomics Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 162 162 1318 1318 90 90 343 343 105 105 749 749 4 4 8 8 361 1083 2418 7254 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=20574125a7381fc9, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef
gtftobed12 gtftobed12 Convert GTF files to BED12 format 2018-05-17 http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README 357 ucsc-gtftogenepred 469 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 3604 4280 9080 10481 3613 3616 9194 9212 390 390 1789 1789 178 178 322 322 7785 24034 20385 62574 https://dev.workflowhub.eu/workflows/1324?version=3, https://dev.workflowhub.eu/workflows/1329?version=5, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.eu/published/workflow?id=cc37667c2d1f9056, https://usegalaxy.eu/published/workflow?id=ccef778cfd9024d1, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=85aede91db0122e4, https://usegalaxy.org.au/published/workflow?id=a1b97364f84022cf, https://usegalaxy.org.au/published/workflow?id=a763e53653b10ce0, https://usegalaxy.org.au/published/workflow?id=ce7f6a1c824920e2, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=044c5ce43f2e1829, https://usegalaxy.org/published/workflow?id=582f3de3971fc38c, https://usegalaxy.org/published/workflow?id=7022c4d9af725e5c, https://usegalaxy.org/published/workflow?id=8c4fcd4bd9d5a72d, https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://workflowhub.eu/workflows/878?version=1 transcriptomics/differential-isoform-expression, transcriptomics/ref-based
gubbins gubbins Gubbins - bacterial recombination detection 2017-06-22 3.2.1 gubbins 3.4 To update Sequence Analysis Genotyping, Phylogenetic inference, Ancestral reconstruction Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing Phylogeny, Genotype and phenotype, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 350 365 3918 4131 246 246 3504 3504 245 301 1876 2618 0 0 0 0 841 2594 9298 28849
gvcftools gvcftools_extract_variants gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. 2016-12-29 https://github.com/sequencing/gvcftools 0.1 gvcftools 0.17.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gwastools gwastools_manhattan_plot 2019-10-07 https://bioconductor.org/packages/release/bioc/html/GWASTools.html 0.1.0 bioconductor-gwastools 1.52.0 To update Visualization, Variant Analysis Deposition, Analysis, Annotation Deposition, Analysis, Annotation GWAS study GWAS study iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 21 21 4 12 21 63 https://usegalaxy.fr/published/workflow?id=1ad87b99f0cb828c
halfdeep halfdeep HalfDeep: Automated detection of intervals covered at half depth by sequenced reads. 2024-11-27 https://github.com/makovalab-psu/HalfDeep 0.1.0 halfdeep 0.1.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 48 48 0 0 0 0 0 0 0 0 2 6 48 144
hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. 2021-02-02 https://github.com/pha4ge/hAMRonization 1.1.4 hamronization 1.1.9 To update Sequence Analysis Data handling, Antimicrobial resistance prediction, Parsing Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Public health and epidemiology, Microbiology, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 270 270 9456 9456 2 2 20 20 0 0 0 0 6 6 15 15 278 834 9491 28473 https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1
hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies 2022-10-19 https://github.com/vibansal/HapCUT2 1.3.4 hapcut2 1.3.4 Up-to-date Assembly Haplotype mapping, Variant classification Haplotype mapping, Variant classification galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 hapcut2 HapCUT2 HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 123 123 0 0 0 0 4 12 123 369
hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes 2022-09-16 https://github.com/institut-de-genomique/HAPO-G 1.3.8 hapog 1.3.8 Up-to-date Assembly Genome assembly, Optimisation and refinement Genome assembly, Optimisation and refinement Sequence assembly, Genomics Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 83 83 636 636 0 0 0 0 0 0 0 0 35 35 367 367 118 354 1003 3009
happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. 2022-01-25 https://github.com/Illumina/hap.py 0.3.14 hap.py 0.3.15 To update Variant Analysis Variant calling, Sequence analysis, Genotyping Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism Genomics, DNA polymorphism iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. 2018-06-11 https://github.com/ls-cwi/heinz 1.0 bioconductor-bionet 1.66.0 To update Transcriptomics, Visualization, Statistics, Single Cell Pathway or network analysis Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks Genetics, Gene expression, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz heinz Heinz Tool for single-species active module discovery. 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 343 447 1201 1440 669 669 1623 1623 55 55 768 768 0 0 0 0 1067 3305 3592 11015 https://dev.workflowhub.eu/workflows/1303?version=1, https://usegalaxy.eu/published/workflow?id=12c80c5b5e2305d8, https://usegalaxy.org.au/published/workflow?id=6a161c87d19a543c transcriptomics/network-analysis-with-heinz
hgvsparser hgvsparser Parsing and building variant descriptor strings compliant with the HGVS standard 2024-06-07 https://github.com/VariantEffect/hgvsParseR/tree/master 0.1.0 r-base To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 6353 6353 0 0 0 0 0 0 0 0 0 0 0 0 2 6 6353 19059
hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hicbuildmatrixmicroc, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. 2017-08-24 https://github.com/deeptools/HiCExplorer 3.7.6 hicexplorer 3.7.6 Up-to-date Sequence Analysis, Visualization bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 38 38 39 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 33 35 33 0 3100 4361 44944 71563 162 162 1516 1516 83 83 2806 2806 1 1 2 2 3346 11299 49268 174423 https://dev.workflowhub.eu/workflows/1181?version=2, https://usegalaxy.eu/published/workflow?id=2f053b615d9788bf, https://usegalaxy.eu/published/workflow?id=5cb54278075696ca, https://usegalaxy.eu/published/workflow?id=8de99510abb6ee7c, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 epigenetics/hicexplorer
hicstuff hicstuff_pipeline A toolkit to generate and manipulate Hi-C matrices 2022-11-25 https://github.com/koszullab/hicstuff 3.2.4 hicstuff 3.2.4 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hifiasm hifiasm A fast haplotype-resolved de novo assembler 2024-07-11 https://github.com/chhylp123/hifiasm 0.25.0 hifiasm 0.25.0 Up-to-date Assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 630 630 2073 2073 438 438 1556 1556 156 156 2960 2960 40 40 108 108 1264 3792 6697 20091 https://dev.workflowhub.eu/workflows/584?version=1, https://dev.workflowhub.eu/workflows/585?version=1, https://dev.workflowhub.eu/workflows/586?version=1, https://usegalaxy.eu/published/workflow?id=002a51bdef00e14d, https://usegalaxy.eu/published/workflow?id=023a0ee62dd1f593, https://usegalaxy.eu/published/workflow?id=03be9d62e8e4a129, https://usegalaxy.eu/published/workflow?id=085c3a4c89d137b5, https://usegalaxy.eu/published/workflow?id=089e5e83b1de0511, https://usegalaxy.eu/published/workflow?id=19bb57f8cfa48bb9, 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hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. 2023-01-18 https://github.com/xfengnefx/hifiasm-meta 0.3.1 hifiasm_meta hamtv0.3.1 To update Metagenomics Sequence assembly Sequence assembly Sequence assembly, Metagenomics Sequence assembly, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 28 28 170 170 0 0 0 0 14 14 287 287 0 0 0 0 42 126 457 1371
hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. 2015-09-29 http://ccb.jhu.edu/software/hisat2/ 2.2.1 hisat2 2.2.1 Up-to-date Assembly Sequence alignment Sequence alignment RNA-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 11045 12103 382199 408162 28038 36924 715633 961962 5368 5997 88949 100616 1039 1039 33708 33729 45490 147043 1220489 3945447 https://dev.workflowhub.eu/workflows/1001?version=1, https://dev.workflowhub.eu/workflows/1042?version=1, https://dev.workflowhub.eu/workflows/1201?version=2, https://dev.workflowhub.eu/workflows/1281?version=1, https://dev.workflowhub.eu/workflows/1295?version=1, 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hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 2018-06-06 https://pypi.org/project/hivclustering/ 1.3.1 python-hivclustering 1.8.0 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). 2015-02-16 http://hmmer.org/ 3.4 hmmer 3.4 Up-to-date Sequence Analysis Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Sequence analysis, Sequence sites, features and motifs, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 1380 1441 37359 38872 0 0 0 0 217 217 3697 3697 116 116 459 462 1713 5200 41515 126061 https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1
htseq_count htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) 2016-09-15 https://readthedocs.org/projects/htseq/ 2.0.5 htseq 2.0.5 Up-to-date Genomic Interval Operations, SAM, Sequence Analysis, RNA Nucleic acid sequence analysis Nucleic acid sequence analysis Sequence analysis Sequence analysis lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 3891 4730 149069 178590 11066 17606 213121 363427 2554 2929 25747 34369 442 442 11046 11063 17953 61613 398983 1385415 https://usegalaxy.eu/published/workflow?id=006ea49456a2a8ca, https://usegalaxy.eu/published/workflow?id=0821ec1cb4d6f30b, https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=0fa523529c4f73cf, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=5b46c8533cd95447, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=70b1c40b818cc320, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=9e03cf8cd5e5de08, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=b6eb5fe7e37f680a, https://usegalaxy.eu/published/workflow?id=c7e1aee909c9b483, https://usegalaxy.eu/published/workflow?id=cf9dc7ad34c81fa2, https://usegalaxy.eu/published/workflow?id=d086340422009ba9, https://usegalaxy.eu/published/workflow?id=e5f6d12e08d7a13b, https://usegalaxy.eu/published/workflow?id=eb3cfa4d1f05fc0e, https://usegalaxy.eu/published/workflow?id=f33b5135ee99e0dc, https://usegalaxy.fr/published/workflow?id=e266db902aa1b0e8, https://usegalaxy.fr/published/workflow?id=ff14dc4005e92cfd, https://usegalaxy.org.au/published/workflow?id=16a2c2e8b3c1ffe6, https://usegalaxy.org.au/published/workflow?id=1a107e6611fb9c15, https://usegalaxy.org.au/published/workflow?id=a35e5a238a70176a, https://usegalaxy.org.au/published/workflow?id=b2818098da6e2f82, https://usegalaxy.org/published/workflow?id=0292971d1a87abba, https://usegalaxy.org/published/workflow?id=204d0da8a023d7da, https://usegalaxy.org/published/workflow?id=385ac7ec85e37e3e, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=413d7e5aa7378cf1, https://usegalaxy.org/published/workflow?id=41c09a87c6cd5f75, https://usegalaxy.org/published/workflow?id=8fb8c80c93ad694e, https://usegalaxy.org/published/workflow?id=a86b1f1682bb4a62, https://usegalaxy.org/published/workflow?id=aafa51fdc172f4c5, https://usegalaxy.org/published/workflow?id=b3823d276917baf0, https://usegalaxy.org/published/workflow?id=ce232859a466c75c, https://usegalaxy.org/published/workflow?id=d2f7fd589a91124a, https://usegalaxy.org/published/workflow?id=d5514e327878b531, https://usegalaxy.org/published/workflow?id=d8afd017905d6702, https://usegalaxy.org/published/workflow?id=dcc7c5fdef8780fd, https://usegalaxy.org/published/workflow?id=dcf6f201b787d148, https://usegalaxy.org/published/workflow?id=e04f443a8ceca0d2, https://usegalaxy.org/published/workflow?id=efb10012b8448b21, https://workflowhub.eu/workflows/412?version=1
humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution 2021-05-12 http://huttenhower.sph.harvard.edu/humann 3.9 humann 3.9 Up-to-date Metagenomics Species frequency estimation, Taxonomic classification, Phylogenetic analysis Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” 6 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 2348 2348 30613 30613 247 247 1226 1226 371 371 4051 4051 8 8 619 619 2974 8922 36509 109527 https://dev.workflowhub.eu/workflows/1080?version=1, https://dev.workflowhub.eu/workflows/1084?version=1, https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=23dd2253da51e22e, https://usegalaxy.eu/published/workflow?id=3118d383c81cf805, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf microbiome/metatranscriptomics, microbiome/metatranscriptomics-short
hybpiper hybpiper Analyse targeted sequence capture data 2023-08-30 https://github.com/mossmatters/HybPiper 2.1.6 hybpiper 2.3.2 To update Sequence Analysis, Phylogenetics Sequence trimming, Sequence assembly, Read mapping Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 1591 1591 0 0 0 0 4 4 187 187 0 0 0 0 8 24 1778 5334
hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies 2018-06-08 http://www.hyphy.org 2.5.47 hyphy 2.5.73 To update Phylogenetics Statistical calculation Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks Phylogeny, Small molecules, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. 17 2 17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 12 17 12 0 473 482 11928 12038 740 740 8092 8092 63 63 794 794 8 8 25 25 1284 3861 20839 62627 https://dev.workflowhub.eu/workflows/43?version=1, https://usegalaxy.eu/published/workflow?id=1d40d6deb2da04cc, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e
hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies 2021-11-15 https://github.com/kensung-lab/hypo 1.0.3 hypo 1.0.3 Up-to-date Assembly Optimisation and refinement, Genome assembly Optimisation and refinement, Genome assembly Sequence assembly, Genomics Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 99 99 505 505 0 0 0 0 0 0 0 0 0 0 0 0 99 297 505 1515 https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1
icescreen icescreen identification of ICEs and IMEs in Bacillota genomes. 2022-01-04 https://forgemia.inra.fr/ices_imes_analysis/icescreen 1.3.3 icescreen 1.3.3 Up-to-date Genome annotation Database search, Protein feature detection Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
idba idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. 2018-04-26 https://i.cs.hku.hk/~alse/hkubrg/projects/index.html idba 1.1.3 To update Assembly Sequence assembly Sequence assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 182 209 1117 1292 288 290 1575 1643 0 0 0 0 3 3 3 3 473 1448 2695 8328
idr idr Galaxy wrappers for the IDR package from Nathan Boleu 2017-08-21 https://github.com/nboley/idr 2.0.3 idr 2.0.4.2 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 117 126 2952 3068 217 217 1863 1863 0 0 0 0 0 0 0 0 334 1011 4815 14561 https://usegalaxy.org/published/workflow?id=59d34b4f0178120b epigenetics/cut_and_run
idr_download_by_ids idr_download_by_ids Image Data Resource downloading tool 2020-02-04 https://idr.openmicroscopy.org 0.45 omero-py 5.11.1 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 39 39 432 432 0 0 0 0 1 1 207 207 0 0 0 0 40 120 639 1917 https://dev.workflowhub.eu/workflows/1262?version=2, https://usegalaxy.eu/published/workflow?id=4a41ea1eb6752171, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://workflowhub.eu/workflows/41?version=2 imaging/2D-spot-detection, imaging/tutorial-CP
iedb_api iedb_api Get epitope binding predictions from IEDB-API 2020-02-26 http://tools.immuneepitope.org/main/tools-api/ 2.15.2 python To update Data Source, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 38 38 1579 1579 2 2 11 11 0 0 0 0 0 0 0 0 40 120 1590 4770 https://dev.workflowhub.eu/workflows/1382?version=1, https://usegalaxy.eu/published/workflow?id=c3f2350f0be2d9c9, https://usegalaxy.org.au/published/workflow?id=832a30759469d3fe, https://usegalaxy.org/published/workflow?id=d0847ce8261eb922 proteomics/neoantigen-7-hla-binding-novel-peptides
infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data 2024-07-23 https://github.com/broadinstitute/infercnv 1.22.0 bioconductor-infercnv 1.22.0 Up-to-date Transcriptomics, Variant Analysis, Single Cell Heat map generation, Expression analysis, RNA-Seq analysis, Copy number variation detection, Clustering Heat map generation, RNA-Seq analysis, Copy number variation detection, Clustering iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv infercnv InferCNV Inferring copy number alterations from tumor single cell RNA-Seq data 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 29 29 0 0 0 0 0 0 0 0 0 0 0 0 5 15 29 87
instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes 2021-08-11 https://instrain.readthedocs.io/en/latest/# 1.5.3 instrain 1.10.0 To update Metagenomics SNP detection, Genome comparison SNP detection, Genome comparison Mapping, Metagenomics Mapping, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 19 19 106 106 0 0 0 0 0 0 0 0 0 0 0 0 19 57 106 318
integronfinder integron_finder "IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching" 2022-09-22 https://github.com/gem-pasteur/Integron_Finder 2.0.5 integron_finder 2.0.6 To update Sequence Analysis Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 280 280 60639 60639 109 109 2299 2299 106 106 7737 7737 28 28 1672 1672 523 1569 72347 217041 https://dev.workflowhub.eu/workflows/1136?version=2, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=9 genome-annotation/bacterial-genome-annotation
intermine_galaxy_exchange galaxy_intermine_exchange InterMine Exporter 2018-07-01 https://github.com/intermine 0.0.1 coreutils 8.25 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 13 30 47 11 15 43 87 1 1 129 129 0 0 0 0 19 67 202 667 https://dev.workflowhub.eu/workflows/1290?version=2 galaxy-interface/intermine
interproscan interproscan Interproscan queries the interpro database and provides annotations. 2021-11-15 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ 5.59-91.0 interproscan 5.59_91.0 To update Sequence Analysis Sequence motif recognition, Protein feature detection Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis Gene and protein families, Sequence analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1916 2027 38987 62864 97 97 502 502 664 664 11896 11896 127 127 9268 9268 2804 8523 60653 205836 https://dev.workflowhub.eu/workflows/1183?version=1, https://dev.workflowhub.eu/workflows/1202?version=1, https://dev.workflowhub.eu/workflows/1357?version=1, https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a95556ec171d405, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://workflowhub.eu/workflows/1262?version=1, https://workflowhub.eu/workflows/754?version=1, https://workflowhub.eu/workflows/755?version=1 ecology/marine_omics_bgc, genome-annotation/funannotate, genome-annotation/functional
interval2maf Interval2Maf1 Extract MAF blocks given a set of intervals 2020-07-14 https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.1+galaxy1 bx-python 0.13.0 To update Genomic Interval Operations Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. 1 1 1 1 0 0 0 0 0 1 0 0 0 0 1 1 1 0 1 0 0 0 0 1 0 0 0 0 0 1 1 1 1 0 7 10 32 107 88 1250 777 19608 2 2 16 24 1 1 1 1 98 1459 826 21392 https://usegalaxy.org/published/workflow?id=7cae620eea6326af, https://usegalaxy.org/published/workflow?id=d3a69b0b826331ef
intervene intervene_pairwise, intervene_upset Create pairwise and upset plots 2018-09-11 https://intervene.readthedocs.io 0.6.5 intervene 0.6.5 Up-to-date Statistics Sequence comparison, Sequence visualisation Sequence comparison, Sequence visualisation Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 332 348 1705 1790 485 485 4628 4628 0 0 0 0 0 0 0 0 817 2467 6333 19084
ipfp_normalisation ipfp_norm Normalisation algorithm used to adjust matrices iteratively to satisfy specific row and column sum constraints while preserving the data structure. 2025-01-28 https://isoquac.net/ 0.1.0+galaxy0 numpy To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation https://github.com/galaxyproject/tools-iuc/tree/main/tools/ipfp_normalisation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
iqtree iqtree Efficient phylogenomic software by maximum likelihood 2017-09-26 http://www.iqtree.org/ 2.4.0 iqtree 2.4.0 Up-to-date Phylogenetics Phylogenetic analysis, Sequence analysis Phylogenetic analysis, Sequence analysis Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1815 1872 34294 34745 2439 2439 27821 27821 946 1074 15740 16435 0 0 0 0 5200 15785 77855 234711 https://dev.workflowhub.eu/workflows/1296?version=2, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=bc5ced57e711acf9, https://usegalaxy.eu/published/workflow?id=d5cf994c03a60fa4, https://usegalaxy.eu/published/workflow?id=e97b938ca4723827, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=952b83e52f7d7cff, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e, https://workflowhub.eu/workflows/1260?version=1, https://workflowhub.eu/workflows/359?version=1 evolution/abc_intro_phylo, sequence-analysis/tapscan-streptophyte-algae, variant-analysis/aiv-analysis
irissv irissv Refine insertion sequences 2021-01-17 https://github.com/mkirsche/Iris 1.0.5 samtools 1.22 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8 8 29 29 0 0 0 0 0 0 0 0 0 0 0 0 8 24 29 87
irma irma Iterative Refinement Meta-Assembler (IRMA) is a tool to construct assembly of highly variable RNA viruses. 2024-11-09 https://wonder.cdc.gov/amd/flu/irma/irma.html 1.2.0 irma 1.2.0 Up-to-date Sequence Analysis Mapping assembly Mapping assembly iuc https://github.com/aaronKol/tools-iuc/tree/main/tools/irma https://github.com/galaxyproject/tools-iuc/tree/main/tools/irma irma-virus IRMA Iterative Refinement Meta-Assembler for robust assembly, variant calling, and phasing of highly variable RNA virus sequencing data 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 7548 7548 0 0 0 0 0 0 0 0 0 0 0 0 2 6 7548 22644
isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. 2022-12-17 https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html 1.20.0 bioconductor-isoformswitchanalyzer 2.6.0 To update Transcriptomics, RNA, Statistics Sequence comparison, Sequence analysis Sequence comparison, Sequence analysis Computational biology, Gene transcripts Computational biology, Gene transcripts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 72 72 1563 1563 95 95 2046 2046 14 14 706 706 1 1 8 8 182 546 4323 12969 https://dev.workflowhub.eu/workflows/1324?version=3, https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930 transcriptomics/differential-isoform-expression
ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing 2020-03-21 https://github.com/andersen-lab/ivar 1.4.4 ivar 1.4.4 Up-to-date Sequence Analysis Primer removal Primer removal Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar andersen-lab_ivar iVar iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. 5 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 4 0 0 0 0 0 5 5 5 0 2611 2611 1311467 1311467 2617 2617 136524 136524 1061 1061 53360 53360 56 56 7296 7296 6345 19035 1508647 4525941 https://dev.workflowhub.eu/workflows/143?version=1, https://dev.workflowhub.eu/workflows/144?version=1, https://dev.workflowhub.eu/workflows/195?version=2, https://dev.workflowhub.eu/workflows/196?version=2, 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https://usegalaxy.org/published/workflow?id=bf90f2bd20fbff21, https://usegalaxy.org/published/workflow?id=c12e6b7896f8e114, https://usegalaxy.org/published/workflow?id=c7b2d2ccc4b0dec5, https://usegalaxy.org/published/workflow?id=d3428dd172a78102, https://usegalaxy.org/published/workflow?id=d4ea6cdd40522eb1, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://usegalaxy.org/published/workflow?id=e282f505ba9f729f, https://workflowhub.eu/workflows/110?version=10, https://workflowhub.eu/workflows/111?version=5, https://workflowhub.eu/workflows/1260?version=1, https://workflowhub.eu/workflows/155?version=5, https://workflowhub.eu/workflows/439?version=2, https://workflowhub.eu/workflows/519?version=1 variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon
iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data 2017-06-08 https://bioconductor.org/packages/release/bioc/html/IWTomics.html 1.0.0 bioconductor-iwtomics 1.30.0 To update Statistics Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Differential gene expression analysis, Peak calling, Genome annotation, Comparison Statistics and probability Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics iwtomics IWTomics Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset. 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 27 28 657 698 29 50 102 252 12 12 446 446 0 0 0 0 68 226 1205 3806 https://dev.workflowhub.eu/workflows/1317?version=2 statistics/iwtomics
jasminesv jasminesv Merge structural variants across samples 2021-01-17 https://github.com/mkirsche/Jasmine/ 1.0.11 jasminesv 1.1.5 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 12 12 38 38 21 21 56 56 0 0 0 0 0 0 0 0 33 99 94 282
jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool 2015-05-01 https://jbrowse.org 1.16.11 jbrowse 1.16.11 Up-to-date Sequence Analysis Genome visualisation Genome visualisation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. 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jcvi_gff_stats jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) 2018-07-31 https://github.com/tanghaibao/jcvi 0.8.4 jcvi 1.5.6 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 672 741 2936 3229 817 818 2611 2613 509 509 1348 1348 38 38 353 353 2036 6178 7248 22039 https://dev.workflowhub.eu/workflows/1164?version=2, https://dev.workflowhub.eu/workflows/1194?version=2, https://dev.workflowhub.eu/workflows/1358?version=2, https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.eu/published/workflow?id=7de6e20699183cd3, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.eu/published/workflow?id=9fb31a16b258cc1a, https://usegalaxy.fr/published/workflow?id=2c823ac083c3cb6d, https://usegalaxy.fr/published/workflow?id=55be36ab73515e65, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=49b253f75ab6f38f, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=65b4051e722228b8, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43, https://workflowhub.eu/workflows/1255?version=2, https://workflowhub.eu/workflows/881?version=5 genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short, genome-annotation/helixer
jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA 2021-04-07 https://github.com/gmarcais/Jellyfish kmer-jellyfish 2.3.1 To update Assembly k-mer counting k-mer counting Sequence analysis, Genomics Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 261 261 1997 1997 0 0 0 0 69 69 1231 1231 31 31 1461 1461 361 1083 4689 14067 https://usegalaxy.eu/published/workflow?id=bc32937d505135ab
join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier 2017-05-31 https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id 1.0 r-data.table 1.11.6 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
jq jq JQ is a lightweight and flexible command-line JSON processor 2017-06-22 https://stedolan.github.io/jq/ 1.0 jq 1.5 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 60 65 599 2377 88 88 352 352 12 12 322 322 3 3 8 8 163 494 1281 5621 https://workflowhub.eu/workflows/245?version=1, https://workflowhub.eu/workflows/373?version=2, https://workflowhub.eu/workflows/374?version=1, https://workflowhub.eu/workflows/375?version=1 galaxy-interface/ncbi-sarf
jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics 2021-02-11 https://lindenb.github.io/jvarkit/ 20201223 jvarkit-wgscoverageplotter 20201223 Up-to-date SAM iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 595 595 8104 8104 1296 1296 13822 13822 0 0 0 0 0 0 0 0 1891 5673 21926 65778 https://usegalaxy.eu/published/workflow?id=cd3398e29f375d97, https://usegalaxy.org/published/workflow?id=3dbe754882a263cd variant-analysis/tb-variant-analysis
kaiju kaiju_addtaxonnames, kaiju_mergeoutputs, kaiju_kaiju, kaiju_kaiju2krona, kaiju_kaiju2table taxonomic classification of high-throughput sequencing reads 2025-04-22 https://github.com/bioinformatics-centre/kaiju 1.10.1 kaiju 1.10.1 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju kaiju Kaiju Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses. 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. 2017-08-04 https://pachterlab.github.io/kallisto/ 0.48.0 kallisto 0.51.1 To update Transcriptomics Gene expression profiling Gene expression profiling Transcriptomics, RNA-Seq, Gene expression Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1069 1154 29732 31465 2599 3240 74251 86306 227 247 5695 6126 21 21 513 513 3916 12494 110191 344792 https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b, https://usegalaxy.eu/published/workflow?id=fd90652d475ed739, https://usegalaxy.org/published/workflow?id=08bdcecd1cb0bda3, https://usegalaxy.org/published/workflow?id=526b05cbffecbc85, https://usegalaxy.org/published/workflow?id=7d9bf3437e0a3d27, https://usegalaxy.org/published/workflow?id=c2c6779a8b1821e0
kc_align kc-align Kc-Align custom tool 2020-02-20 https://github.com/davebx/kc-align 1.0.2 kcalign 1.0.2 Up-to-date Sequence Analysis Multiple sequence alignment Multiple sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments. Kc-Align is a codon-aware multiple aligner that uses Kalgin2 to produce in-frame gapped codon alignments for selection analysis of small genomes (mostly viral and some smaller bacterial genomes). Takes nucleotide seqeunces as inputs, converts them to their in-frame amino acid sequences, performs multiple alignment with Kalign, and then converts the alignments back to their original codon sequence while preserving the gaps. Produces three outputs: the gapped nucleotide alignments in FASTA format and in CLUSTAL format and the amino acid level alignment.Kc-Align will also attempt to detect any frameshift mutations in the input reads. If a frameshift is detected, that sequence will not be included in the multiple alignment and its ID will be printed to stdout. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 55 382 382 279 279 8306 8306 0 0 0 0 0 0 0 0 334 1002 8688 26064 https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e
khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more 2015-03-24 https://khmer.readthedocs.org/ 3.0.0a3 khmer 3.0.0a3 Up-to-date Assembly, Next Gen Mappers Standardisation and normalisation, De-novo assembly Standardisation and normalisation, De-novo assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 8 8 8 0 186 213 1775 2145 411 411 1508 1509 64 64 1845 1845 0 0 0 0 661 2010 5128 15755
king king Kinship-based INference for Gwas 2021-11-16 http://people.virginia.edu/~wc9c/KING/ 2.2.7 king 2.2.7 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/king 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 8 8 0 0 0 0 0 0 0 0 0 0 0 0 4 12 8 24
kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) 2022-09-09 https://github.com/katholt/Kleborate/wiki 2.3.2 kleborate 3.1.3 To update Metagenomics Multilocus sequence typing, Genome assembly, Virulence prediction Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 74 74 650 650 0 0 0 0 0 0 0 0 0 0 0 0 74 222 650 1950
kma kma_map Map with KMA 2019-10-30 https://bitbucket.org/genomicepidemiology/kma 1.4.14 kma 1.5.0 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 3 https://workflowhub.eu/workflows/407?version=1
kmer2stats kmer2stats A tool for creating data files for statistics based on kmers 2025-04-16 https://github.com/SantaMcCloud/kmer2stats 1.0.1 kmer2stats 1.0.1 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/kmer2stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model 2020-11-12 https://github.com/takaram/kofam_scan 1.3.0 kofamscan 1.3.0 Up-to-date Sequence Analysis Sequence analysis, Gene functional annotation Sequence analysis, Gene functional annotation Genomics, Structure analysis Genomics, Structure analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 74 74 1643 1643 0 0 0 0 0 0 0 0 2 2 3 3 76 228 1646 4938 https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=d57d41e306241396
kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. 2017-01-24 http://ccb.jhu.edu/software/kraken/ kraken 1.1.1 To update Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics Taxonomy, Metagenomics devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. 5 5 5 5 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 3071 3078 59088 59121 5897 9180 58182 136649 1874 2393 31342 35855 241 241 1805 1805 11083 37058 150417 534264 https://usegalaxy.eu/published/workflow?id=201e65bcf2b71584, https://usegalaxy.org/published/workflow?id=2ec3e326c51d3147, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=7321c6ad5425d347, https://usegalaxy.org/published/workflow?id=a89e1018a00b883c, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be
kraken2 kraken2 Kraken2 for taxonomic designation. 2019-03-05 http://ccb.jhu.edu/software/kraken/ 2.1.3 kraken2 2.14 To update Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.Any assumption that Kraken’s raw read assignments can be directly translated into species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN), estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree. 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kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) 2022-09-03 https://github.com/smdabdoub/kraken-biom 1.2.0 kraken-biom 1.2.0 Up-to-date Metagenomics Genome annotation, Taxonomic classification Genome annotation, Taxonomic classification Metagenomics, Taxonomy Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom kraken-biom kraken-biom Create BIOM-format tables from Kraken output 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 600 600 3832 3832 0 0 0 0 64 64 599 599 4 4 6 6 668 2004 4437 13311 https://dev.workflowhub.eu/workflows/1095?version=1, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=a0ea6fc756dd17ea, https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 microbiome/taxonomic-profiling
kraken_taxonomy_report kraken_taxonomy_report Kraken taxonomy report 2016-06-01 https://github.com/blankenberg/Kraken-Taxonomy-Report 0.0.3 biopython 1.70 To update Metagenomics Visualisation, Classification Visualisation, Classification Metagenomics, Taxonomy Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 879 882 4542 4551 1084 1435 4573 6288 73 73 175 175 0 0 0 0 2036 6462 9290 29594 https://usegalaxy.eu/published/workflow?id=2e5e6291cd112225, https://usegalaxy.eu/published/workflow?id=b659069edd9b1d4e
krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken 2023-01-13 https://github.com/jenniferlu717/KrakenTools 1.2 krakentools 1.2 Up-to-date Metagenomics Visualisation, Aggregation Visualisation, Aggregation Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 3231 3231 107718 107718 1814 1814 21868 21868 577 577 9815 9815 57 57 494 494 5679 17037 139895 419685 https://dev.workflowhub.eu/workflows/1073?version=1, https://dev.workflowhub.eu/workflows/1087?version=2, https://dev.workflowhub.eu/workflows/1095?version=1, https://dev.workflowhub.eu/workflows/1097?version=1, https://dev.workflowhub.eu/workflows/1349?version=1, https://usegalaxy.eu/published/workflow?id=0590554db9794d13, https://usegalaxy.eu/published/workflow?id=10101558b211a782, https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c, https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=b37800d990cceb83, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=ed2df13cfbc86b99, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=131636a795bac485, https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b, https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2, https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, https://usegalaxy.org.au/published/workflow?id=d9ba165e6ae55417, https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56, https://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38b, https://usegalaxy.org/published/workflow?id=574e42683dc3961b, https://usegalaxy.org/published/workflow?id=60f0d0d5d6e93941, https://usegalaxy.org/published/workflow?id=7321c6ad5425d347, https://usegalaxy.org/published/workflow?id=8f5904693b5f74f4, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1059?version=1, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1199?version=2 microbiome/beer-data-analysis, microbiome/diversity, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling
krocus krocus Predict MLST directly from uncorrected long reads 2019-09-03 https://github.com/quadram-institute-bioscience/krocus 1.0.1 krocus 1.0.3 To update Sequence Analysis Multilocus sequence typing, k-mer counting Multilocus sequence typing, k-mer counting Public health and epidemiology Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus krocus krocus Predict MLST directly from uncorrected long reads 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
last last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. 2020-06-17 http://last.cbrc.jp/ 1205 last 1639 To update Sequence Analysis Sequence alignment Sequence alignment Genomics, Comparative genomics Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last last LAST Short read alignment program incorporating quality scores 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 100 100 361 361 0 0 0 0 0 0 0 0 11 11 22 22 111 333 383 1149
lastz lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d 2018-02-12 https://github.com/lastz/lastz 1.04.22 lastz 1.04.52 To update Next Gen Mappers Sequence alignment, Read mapping Sequence alignment, Read mapping Genomics Genomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 471 513 72800 84650 828 3558 155447 196753 172 209 38622 38995 13 13 4662 4662 1484 7261 271531 868122 https://dev.workflowhub.eu/workflows/1113?version=2, https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5 assembly/ecoli_comparison
lcrgenie lcrgenie Ligase Chain Reaction Genie 2022-12-02 https://github.com/neilswainston/LCRGenie 1.0.2 lcr_genie To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
legsta legsta Performs in silico Legionella pneumophila sequence based typing. 2022-02-21 https://github.com/tseemann/legsta 0.5.1 legsta 0.5.1 Up-to-date Sequence Analysis Sequence analysis Sequence analysis Public health and epidemiology Public health and epidemiology iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 103 103 0 0 0 0 0 0 0 0 0 0 0 0 9 27 103 309
length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file 2016-11-13 https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 To update Fasta Manipulation, Statistics, RNA, Micro-array Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 795 834 4656 4801 1088 1191 2312 2607 89 89 242 242 5 5 7 7 1977 6073 7217 22091 https://dev.workflowhub.eu/workflows/1326?version=3, https://dev.workflowhub.eu/workflows/1329?version=5, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.org.au/published/workflow?id=2cef9a1633e0a067 transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz
limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline 2017-05-24 http://bioconductor.org/packages/release/bioc/html/limma.html 3.58.1 bioconductor-limma 3.62.1 To update Transcriptomics, RNA, Statistics RNA-Seq analysis RNA-Seq analysis Molecular biology, Genetics Molecular biology, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom limma limma Data analysis, linear models and differential expression for microarray data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2653 2800 25289 26939 4842 5568 48656 54386 923 947 9863 10425 22 22 289 289 8440 26217 84097 260233 https://dev.workflowhub.eu/workflows/1321?version=1, https://dev.workflowhub.eu/workflows/1332?version=1, https://usegalaxy.eu/published/workflow?id=09c77b6fc5add851, https://usegalaxy.eu/published/workflow?id=14226641bba951f3, https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=1c1083b159e5bfb2, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=227d97974573aaf2, https://usegalaxy.eu/published/workflow?id=263eed267aa3e76b, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2ecf737b53f77cf8, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=2f7c04ad219a9d2d, https://usegalaxy.eu/published/workflow?id=3386856a60b35897, https://usegalaxy.eu/published/workflow?id=47f2c44d79896f08, https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6d47a24218d08930, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=7036a6cf67d53bc7, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=8ab363878cd34ef0, https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37, https://usegalaxy.eu/published/workflow?id=8f095e5b9594b098, https://usegalaxy.eu/published/workflow?id=9a83043d5e847318, https://usegalaxy.eu/published/workflow?id=ad3be77eb2e8c10e, https://usegalaxy.eu/published/workflow?id=bb4ecac751a94c79, https://usegalaxy.eu/published/workflow?id=c8deb8952abce1ec, https://usegalaxy.eu/published/workflow?id=d6eb0562d0036940, https://usegalaxy.eu/published/workflow?id=f9ddc4dd9140b293, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.eu/published/workflow?id=fe6c64676be56ee9, https://usegalaxy.org.au/published/workflow?id=bdb498b1f0e8944f, https://usegalaxy.org/published/workflow?id=07fdeadce7a6d5cb, https://usegalaxy.org/published/workflow?id=092be3cf6e40282c, https://usegalaxy.org/published/workflow?id=0a009cf9e88171f1, https://usegalaxy.org/published/workflow?id=0c052e50594f6d2d, https://usegalaxy.org/published/workflow?id=204d0da8a023d7da, https://usegalaxy.org/published/workflow?id=228ae7f537a60226, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=427fce51fd9508eb, https://usegalaxy.org/published/workflow?id=43c39bc86399188f, https://usegalaxy.org/published/workflow?id=5203bc68df3cf819, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=93650de42fb8c015, https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=b3823d276917baf0, https://usegalaxy.org/published/workflow?id=d5514e327878b531, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=dec0cf06fa059e65, https://workflowhub.eu/workflows/689?version=1 transcriptomics/minerva-pathways, transcriptomics/rna-seq-counts-to-genes
lineagespot lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) 2023-07-04 https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html 1.6.0 r-base To update Metagenomics, Sequence Analysis Variant calling Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 39 39 0 0 0 0 0 0 0 0 0 0 0 0 4 12 39 117
links links Scaffold genome assemblies with long reads. 2022-02-23 https://github.com/bcgsc/LINKS 2.0.1 links 2.0.1 Up-to-date Assembly Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Sequence assembly, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 139 139 648 648 0 0 0 0 72 72 577 577 0 0 0 0 211 633 1225 3675
lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. 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https://usegalaxy.org/published/workflow?id=fe4c2791508c56ab, https://usegalaxy.org/published/workflow?id=fff1a5c7475b3eeb, https://workflowhub.eu/workflows/394?version=1, https://workflowhub.eu/workflows/395?version=15, https://workflowhub.eu/workflows/397?version=13, https://workflowhub.eu/workflows/398?version=14, https://workflowhub.eu/workflows/399?version=19, https://workflowhub.eu/workflows/561?version=11 epigenetics/atac-seq, epigenetics/cut_and_run, epigenetics/estrogen-receptor-binding-site-identification, epigenetics/formation_of_super-structures_on_xi, epigenetics/tal1-binding-site-identification, single-cell/scatac-preprocessing-tenx
maf_stats maf_stats1 MAF Coverage statistics 2020-08-12 https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.2+galaxy0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1 1 1 1 0 1 0 0 0 1 1 0 0 0 1 1 1 0 1 0 0 0 0 1 1 0 0 0 1 1 1 1 1 0 7 9 15 21 53 467 194 2479 1 1 1 1 0 0 0 0 61 599 210 2921
maf_tools ucsc_mafaddirows Utilities for working with MAF (Multiple Alignment Format) files from UCSC 2025-06-03 http://genome.ucsc.edu 469 ucsc-mafaddirows 469 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. 2017-11-08 https://sourceforge.net/projects/mageck/ 0.5.9.2 mageck 0.5.9.5 To update Genome editing Genetic variation analysis Genetic variation analysis Genetics, Genetic variation, Genomics Genetics, Genetic variation, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 945 968 12805 13389 753 753 8908 8908 350 356 6252 6356 4 4 8 8 2052 6185 27973 84607 https://dev.workflowhub.eu/workflows/1179?version=2 genome-annotation/crispr-screen
magicblast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome 2022-04-05 https://ncbi.github.io/magicblast/ 1.7.0 magicblast 1.7.0 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 188 188 6949 6949 0 0 0 0 1 1 2 2 0 0 0 0 189 567 6951 20853
maker maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. 2017-10-04 http://www.yandell-lab.org/software/maker.html 2.31.11 maker 3.01.03 To update Sequence Analysis Genome annotation Genome annotation Genomics, DNA, Sequence analysis Genomics, DNA, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1460 1564 6686 7557 2048 2048 9650 9650 930 930 4410 4410 28 28 129 129 4466 13502 20875 63496 https://dev.workflowhub.eu/workflows/1164?version=2, https://dev.workflowhub.eu/workflows/1194?version=2, https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=65b4051e722228b8, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43 genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short
malt_run malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. 2021-11-12 https://github.com/husonlab/malt 0.5.3 malt 0.62 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 25 25 0 0 0 0 0 0 0 0 0 0 0 0 9 27 25 75
map_param_value map_param_value Map a parameter value to another value 2022-10-13 0.2.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 112 112 4503 4503 114 114 2410 2410 4 4 129 129 0 0 0 0 230 690 7042 21126 https://usegalaxy.eu/published/workflow?id=0603f0898211f806, https://usegalaxy.eu/published/workflow?id=0eb137cd936bbfe0, https://usegalaxy.eu/published/workflow?id=18af9bbae833f8fe, https://usegalaxy.eu/published/workflow?id=249c5d6698c8b98c, https://usegalaxy.eu/published/workflow?id=2d08a73dd8ff99e9, https://usegalaxy.eu/published/workflow?id=373d861ef4b0081a, https://usegalaxy.eu/published/workflow?id=406e6ef0dfb38628, https://usegalaxy.eu/published/workflow?id=409336bf210033a2, https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68, 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maplot maplot Generate MA plots for visualizing data distributions using Plotly or Matplotlib. 2025-04-17 https://github.com/galaxyproject/tools-iuc 1.0.0 plotly To update Visualization, Statistics iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maplot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. 2023-08-02 https://github.com/jfmrod/MAPseq 2.1.1b perl To update Metagenomics k-mer counting k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 9212 9212 4 4 17 17 0 0 0 0 0 0 0 0 52 156 9229 27687 https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977, https://usegalaxy.eu/published/workflow?id=169327ba670607d1, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://workflowhub.eu/workflows/1270?version=1, https://workflowhub.eu/workflows/1273?version=1
mash mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash 2018-12-07 https://github.com/marbl/Mash 2.3 mash 2.3 Up-to-date Metagenomics Sequence distance matrix generation Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash mash Mash Fast genome and metagenome distance estimation using MinHash. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 64 64 10171 10171 12 12 333 333 12 12 1980 1980 2 2 21 21 90 270 12505 37515
mashmap mashmap Fast local alignment boundaries 2024-02-26 https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap 3.1.3 mashmap 3.1.3 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 1301 1301 17 17 990 990 0 0 0 0 0 0 0 0 38 114 2291 6873 https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=5aaa64ecdf9f7d6e, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=f9a73b39b2051af1
masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments 2017-05-09 https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html 1.49.3 coreutils 8.25 To update Transcriptomics, RNA, Statistics Regression analysis Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq Gene expression, Microarray experiment, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 42 376 584 83 83 602 602 0 0 0 0 0 0 0 0 118 361 978 3142
maxbin2 maxbin2 clusters metagenomic contigs into bins 2019-10-24 https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html maxbin2 2.2.7 To update Metagenomics Sequence assembly Sequence assembly Metagenomics, Sequence assembly, Microbiology Metagenomics, Sequence assembly, Microbiology mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 360 366 3368 3444 568 572 2616 2625 91 91 1002 1002 4 4 620 620 1023 3079 7606 22903 https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=b0377f05f97b18b1, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef
mcl mcl The Markov Cluster Algorithm, a cluster algorithm for graphs 2022-05-12 https://micans.org/mcl/man/mcl.html 22.282 mcl 22.282 Up-to-date Sequence Analysis Clustering, Network analysis, Gene regulatory network analysis Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 18 153 153 0 0 0 0 0 0 0 0 0 0 0 0 18 54 153 459
medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research 2020-02-23 https://github.com/nanoporetech/medaka 1.7.2 medaka 2.1.0 To update Sequence Analysis Base-calling, Variant calling, Sequence assembly Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning Sequence assembly, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 0 0 0 0 3 3 3 0 1895 1895 126369 126369 980 980 59930 59930 708 708 10431 10431 43 43 2510 2510 3626 10878 199240 597720 https://dev.workflowhub.eu/workflows/1091?version=1, https://dev.workflowhub.eu/workflows/1174?version=2, https://dev.workflowhub.eu/workflows/144?version=1, https://dev.workflowhub.eu/workflows/195?version=2, https://usegalaxy.eu/published/workflow?id=0f6a7bd5362e4a2b, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2d9d4445a1871230, https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef, https://usegalaxy.eu/published/workflow?id=429ae28a178cd07c, https://usegalaxy.eu/published/workflow?id=476db04368d5e90c, https://usegalaxy.eu/published/workflow?id=4d97068a725c975c, https://usegalaxy.eu/published/workflow?id=529f30e894beacc2, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=70d3ebf31940bfb3, https://usegalaxy.eu/published/workflow?id=77e5bbd317750915, https://usegalaxy.eu/published/workflow?id=7bdd9ad918edab0b, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=b97532c398b821a2, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=cf8591391a17a914, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.fr/published/workflow?id=61235264d5d2f666, https://usegalaxy.fr/published/workflow?id=727cfdb7c79287d1, https://usegalaxy.fr/published/workflow?id=e3c04a30258421aa, https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060, https://usegalaxy.org.au/published/workflow?id=0c6f7bfc826433c4, https://usegalaxy.org.au/published/workflow?id=47ce6a2d30887637, https://usegalaxy.org.au/published/workflow?id=48a60965b6b3ff54, https://usegalaxy.org.au/published/workflow?id=4bc8ac41ecff7daf, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=705658f68ae73930, https://usegalaxy.org.au/published/workflow?id=888f8377eb6eabf2, https://usegalaxy.org.au/published/workflow?id=932bad88f8dc8d33, https://usegalaxy.org.au/published/workflow?id=ba7a9d4c857d26b7, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5, https://usegalaxy.org/published/workflow?id=4357180d40560019, https://usegalaxy.org/published/workflow?id=88d0b64011c3148c, https://usegalaxy.org/published/workflow?id=953d9cbe05e632a8, https://usegalaxy.org/published/workflow?id=9adf8691809326e5, https://usegalaxy.org/published/workflow?id=c12e6b7896f8e114, https://usegalaxy.org/published/workflow?id=c7b2d2ccc4b0dec5, https://usegalaxy.org/published/workflow?id=cce88bc57b180d09, https://usegalaxy.org/published/workflow?id=d3428dd172a78102, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/111?version=5, https://workflowhub.eu/workflows/226?version=1 assembly/largegenome, microbiome/pathogen-detection-from-nanopore-foodborne-data
megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. 2017-09-22 https://github.com/voutcn/megahit 1.2.9 megahit 1.2.9 Up-to-date Sequence Analysis, Assembly, Metagenomics Genome assembly Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Metagenomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 0 1 1 1 0 1635 1720 14667 16136 2453 2464 19200 19231 506 506 7542 7542 31 31 1147 1147 4625 13971 42556 129168 https://dev.workflowhub.eu/workflows/1099?version=1, https://dev.workflowhub.eu/workflows/1103?version=1, https://dev.workflowhub.eu/workflows/1116?version=1, https://dev.workflowhub.eu/workflows/1120?version=1, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=534f5fc25bc887ca, https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=b37800d990cceb83, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893 assembly/metagenomics-assembly, microbiome/metagenomics-assembly, microbiome/metagenomics-binning
megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) 2018-11-09 https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp 1.1.3 megahit 1.2.9 To update Sequence Analysis, Assembly, Metagenomics Genome assembly Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Metagenomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 171 175 566 619 67 67 188 188 17 17 76 76 3 3 44 44 258 778 874 2675 https://dev.workflowhub.eu/workflows/1103?version=1, https://dev.workflowhub.eu/workflows/1120?version=1, https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3 assembly/metagenomics-assembly, microbiome/metagenomics-assembly
megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). 2021-11-24 https://github.com/husonlab/megan-ce 6.21.7 megan 6.25.10 To update Sequence Analysis Sequence analysis, Taxonomic classification Sequence analysis, Taxonomic classification Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzerÂť) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. 0 1 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 507 507 4619 4619 0 0 0 0 0 0 0 0 0 0 0 0 507 1521 4619 13857
meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. 2015-12-13 http://meme-suite.org/ 5.5.6 meme 5.5.8 To update ChIP-seq Nucleic acid feature detection, Protein feature detection, Statistical calculation Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability Data mining, Sequence analysis, Genetic variation, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme meme_meme meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. 3 0 4 0 0 0 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 4 0 780 944 21108 23489 1584 3477 10807 26966 0 0 0 0 0 3 0 150 2364 9152 31915 114435 https://usegalaxy.org/published/workflow?id=ecb279a9114140ab
meme_chip meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. 2018-03-15 http://meme-suite.org/ 4.11.2 graphicsmagick 1.3.26 To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 741 818 6420 7338 1283 1287 7778 7795 0 0 0 0 0 0 0 0 2024 6153 14198 43529 https://dev.workflowhub.eu/workflows/1285?version=2, https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=ad4b347f9b68e127, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://usegalaxy.org/published/workflow?id=59d34b4f0178120b epigenetics/cut_and_run, transcriptomics/clipseq
meningotype meningotype Assign sequence type to N. meningitidis genome assemblies 2023-06-06 https://github.com/MDU-PHL/meningotype 0.8.5 meningotype 0.8.5 Up-to-date Sequence Analysis Genotyping, Multilocus sequence typing Multilocus sequence typing Microbiology, Genotype and phenotype Microbiology, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
merlin merlin Pedigree Analysis package 2020-04-15 http://csg.sph.umich.edu/abecasis/Merlin/ 1.1.2 merlin 1.1.2 Up-to-date Variant Analysis Haplotype mapping, Genetic mapping Haplotype mapping GWAS study, Mapping GWAS study, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. 2021-04-18 https://github.com/marbl/merqury 1.3 merqury 1.3 Up-to-date Assembly Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Sequence assembly, Whole genome sequencing, Plant biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 561 561 3593 3593 239 239 1048 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merquryfk merquryfk_asmplot, merquryfk_cnplot, merquryfk_hapmaker, merquryfk_happlot, merquryfk_merquryfk FastK based version of Merqury 2025-02-11 https://github.com/thegenemyers/MERQURY.FK 1.1.1 merquryfk 1.1.2 To update Sequence Analysis, Assembly iuc https://github.com/thegenemyers/MERQURY.FK https://github.com/galaxyproject/tools-iuc/tree/main/tools/merquryfk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. 2021-04-05 https://github.com/marbl/meryl 1.3 merqury 1.3 Up-to-date Assembly k-mer counting k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Whole genome sequencing, Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. 7 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 38 38 209 209 0 0 0 0 0 0 0 0 39 117 211 633 https://usegalaxy.org/published/workflow?id=5503f7835226bc04, https://usegalaxy.org/published/workflow?id=83898f7cbfb7f88e, https://workflowhub.eu/workflows/631?version=5, https://workflowhub.eu/workflows/632?version=8
metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. 2022-01-28 https://bitbucket.org/berkeleylab/metabat/src/master/ 2.17 metabat2 2.18 To update Metagenomics Read binning, Sequence assembly, Genome annotation Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Metagenomics, Sequence assembly, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 MetaBAT_2 MetaBAT 2 an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning 2 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 562 562 8413 8413 241 241 1312 1312 126 126 1248 1248 19 19 1281 1281 948 2844 12254 36762 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=b0377f05f97b18b1
metabuli metabuli_classify Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences 2024-06-04 https://github.com/steineggerlab/Metabuli 1.0.5 metabuli 1.1.0 To update Sequence Analysis, Metagenomics Taxonomic classification Taxonomic classification Taxonomy Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli metabuli metabuli Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 2020-08-04 https://github.com/soedinglab/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 To update Sequence Analysis, Genome annotation Homology-based gene prediction Homology-based gene prediction Metagenomics, Gene and protein families Metagenomics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 50 50 496 496 0 0 0 0 0 0 0 0 0 0 0 0 50 150 496 1488 https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92
metagenomeseq_normalization metagenomeseq_normalizaton metagenomeSeq Normalization 2017-03-27 https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 To update Metagenomics Sequence visualisation, Statistical calculation Sequence visualisation, Statistical calculation Metagenomics, Sequencing Metagenomics, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 17 23 546 762 31 56 290 526 0 0 0 0 0 0 0 0 48 175 836 2960
metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis 2021-03-11 https://github.com/biobakery/MetaPhlAn 4.1.1 metaphlan 4.2.2 To update Metagenomics Taxonomic classification, Taxonomic classification Taxonomic classification, Taxonomic classification Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. 1 2 4 4 0 0 0 0 0 0 0 0 0 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 1 4 4 0 1395 1400 21392 21426 797 797 10266 10266 305 305 5248 5248 12 12 148 148 2509 7532 37054 111196 https://dev.workflowhub.eu/workflows/1088?version=1, https://dev.workflowhub.eu/workflows/1095?version=1, https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.org.au/published/workflow?id=6b7e565258a9da2a, https://workflowhub.eu/workflows/624?version=1 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/taxonomic-profiling
metawrapmg_binning metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis 2024-04-11 https://github.com/bxlab/metaWRAP 1.3.0 metawrap-mg 1.3.0 Up-to-date Metagenomics Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Whole genome sequencing, Metagenomic sequencing, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 66 66 437 437 0 0 0 0 60 60 485 485 0 0 0 0 126 378 922 2766
mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 2024-07-12 https://github.com/EBI-Metagenomics/emg-toolkit 0.10.4 mg-toolkit 0.10.4 Up-to-date Metagenomics Data retrieval Data retrieval Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 13 13 0 0 0 0 0 0 0 0 0 0 0 0 8 24 13 39
microsatbed microsatbed Select microsatellites for a bed file 2024-07-21 https://github.com/lmdu/pytrf 1.3.3 python To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 928 928 9 9 689 689 0 0 0 0 0 0 0 0 19 57 1617 4851 https://usegalaxy.eu/published/workflow?id=3b94f511c52da835
migmap migmap mapper for full-length T- and B-cell repertoire sequencing 2017-09-29 https://github.com/mikessh/migmap 1.0.3 migmap 1.0.3 Up-to-date RNA, Sequence Analysis Sequence analysis, Read mapping Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 34 1030 1232 73 95 1087 1452 0 0 0 0 0 0 0 0 99 327 2117 6918
minia minia Short-read assembler based on a de Bruijn graph 2020-04-08 https://gatb.inria.fr/software/minia/ 3.2.6 minia 3.2.6 Up-to-date Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 267 267 7144 7144 0 0 0 0 71 71 316 316 0 0 0 0 338 1014 7460 22380 https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40
miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) 2019-06-18 https://github.com/lh3/miniasm 0.3_r179 miniasm 0.3 To update Assembly De-novo assembly De-novo assembly Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 605 643 12146 14127 501 502 9362 9371 90 90 1063 1063 12 12 147 147 1208 3663 22718 70144 https://dev.workflowhub.eu/workflows/1107?version=1, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://workflowhub.eu/workflows/406?version=1 microbiome/plasmid-metagenomics-nanopore
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miniprot miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. 2022-09-19 https://github.com/lh3/miniprot 0.13 miniprot 0.16 To update Sequence Analysis Sequence alignment, Protein sequence analysis Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Sequence sites, features and motifs, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 127 127 4896 4896 48 48 275 275 0 0 0 0 24 24 191 191 199 597 5362 16086 https://usegalaxy.eu/published/workflow?id=0c92c3c322c3effe
mirmachine mirmachine Tool to detect miRNA in genome sequences 2024-03-15 https://github.com/sinanugur/MirMachine 0.3.0 mirmachine 0.3.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 7 7 0 0 0 0 0 0 0 0 0 0 0 0 5 15 7 21
mirnature mirnature Computational detection of canonical microRNAs 2022-12-11 https://github.com/Bierinformatik/miRNAture 1.1 mirnature 1.1 Up-to-date RNA, Sequence Analysis iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 22 22 0 0 0 0 0 0 0 0 0 0 0 0 10 30 22 66
mitobim mitobim assemble mitochondrial genomes 2020-12-29 https://github.com/chrishah/MITObim 1.9.1 mitobim 1.9.1 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 151 151 1293 1293 0 0 0 0 30 30 394 394 0 0 0 0 181 543 1687 5061
mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes 2020-02-18 http://mitos.bioinf.uni-leipzig.de/ 1.1.7 mitos 2.1.9 To update Sequence Analysis Genome annotation Genome annotation Zoology, Whole genome sequencing Zoology, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos mitos MITOS De novo metazoan mitochondrial genome annotation. 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 1378 1378 245668 245668 479 479 64235 64235 103 103 12954 12954 0 0 0 0 1960 5880 322857 968571 https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10
mlst mlst, mlst_list Scan contig files against PubMLST typing schemes 2016-12-12 https://github.com/tseemann/mlst 2.22.0 mlst 2.23.0 To update Sequence Analysis Multilocus sequence typing Multilocus sequence typing Immunoproteins and antigens Immunoproteins and antigens iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1681 1757 20225 20983 1404 1404 8326 8326 1192 1479 10742 12950 20 20 82 82 4297 13254 39375 121091 https://usegalaxy.eu/published/workflow?id=201e65bcf2b71584, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=e20172eb0f30d6cd, https://usegalaxy.org/published/workflow?id=675d70ee099dd3f2, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be microbiome/pathogen-detection-from-nanopore-foodborne-data
mmseqs2 mmseqs2_easy_linclust_clustering, mmseqs2_taxonomy_assignment MMseqs2 is an ultra fast and sensitive sequence search and clustering suite 2025-03-27 https://github.com/soedinglab/MMseqs2 17-b804f mmseqs2 17.b804f To update Sequence Analysis, Metagenomics Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification Metagenomics, Sequence analysis, Proteins, Nucleic acids, Gene and protein families, Taxonomy Metagenomics, Sequence analysis, Nucleic acids, Gene and protein families, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmseqs2 MMseqs2 MMseqs2 MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mmuphin mmuphin MMUPHin is an R package implementing meta-analysis methods for microbial community profiles 2024-11-22 https://huttenhower.sph.harvard.edu/mmuphin 1.16.0 bioconductor-mmuphin 1.16.0 Up-to-date Metagenomics iuc https://github.com/biobakery/MMUPHin https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmuphin mmuphin mmuphin MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
moabs moabs MOABS for differential methylation analysis on Bisulfite sequencing data. 2019-07-28 https://github.com/sunnyisgalaxy/moabs 1.3.4.6 moabs 1.3.9.6 To update Epigenetics iuc https://github.com/sunnyisgalaxy/moabs https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 52 57 298 349 0 0 0 0 0 0 0 0 0 0 0 0 52 161 298 945
mosdepth mosdepth fast and flexible BAM/CRAM depth calculation 2022-12-04 https://github.com/brentp/mosdepth 0.3.10 mosdepth 0.3.10 Up-to-date SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 123 123 6665 6665 76 76 11721 11721 18 18 1793 1793 1 1 1500 1500 218 654 21679 65037 https://dev.workflowhub.eu/workflows/1069?version=2, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.org/published/workflow?id=0c6dbb2ef5eee5b9, https://usegalaxy.org/published/workflow?id=695d20ef3ee4cf1e, https://usegalaxy.org/published/workflow?id=779ea0b19d07a1bd, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1 variant-analysis/tb-variant-analysis
mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers 2016-06-24 https://www.mothur.org 1.0 mothur 1.48.3 To update Metagenomics DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny Microbial ecology, Taxonomy, Sequence analysis, Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities 129 129 129 129 0 0 0 0 0 0 0 0 0 0 0 128 0 3 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 38521 44483 295232 338504 72529 94717 517658 713565 27402 29877 168564 196553 2407 2407 14049 14049 140859 453202 995503 3253677 https://dev.workflowhub.eu/workflows/1060?version=1, https://dev.workflowhub.eu/workflows/1070?version=1, https://dev.workflowhub.eu/workflows/1101?version=1, https://dev.workflowhub.eu/workflows/1112?version=1, https://dev.workflowhub.eu/workflows/1117?version=1, https://dev.workflowhub.eu/workflows/1121?version=1, 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https://workflowhub.eu/workflows/652?version=1, https://workflowhub.eu/workflows/653?version=1 microbiome/general-tutorial, microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short, sequence-analysis/Manage_AB1_Sanger
msaboot msaboot A multiple sequences alignment bootstrapping tool. 2018-02-12 https://github.com/phac-nml/msaboot 0.1.2 msaboot 0.1.2 Up-to-date Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 100 112 936 1028 187 189 1138 1141 0 0 0 0 0 0 0 0 287 875 2074 6317
multigps multigps Analyzes collections of multi-condition ChIP-seq data. 2017-03-06 http://mahonylab.org/software/multigps/ 0.74.0 fonts-conda-ecosystem To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 141 301 417 886 0 0 0 0 0 0 0 0 141 583 417 1720
multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data 2023-06-07 https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html 1.12.0 bioconductor-multigsea 1.16.0 To update Transcriptomics, Proteomics, Statistics, Single Cell Gene-set enrichment analysis, Aggregation, Pathway analysis Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 44 44 159 159 0 0 0 0 0 0 0 0 0 0 0 0 44 132 159 477 proteomics/multiGSEA-tutorial
multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report 2017-09-21 http://multiqc.info/ 1.27 multiqc 1.29 To update Fastq Manipulation, Statistics, Visualization Validation, Sequencing quality control Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics Sequencing, Bioinformatics, Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. 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https://workflowhub.eu/workflows/876?version=1 assembly/assembly-with-preprocessing, assembly/general-introduction, assembly/largegenome, assembly/unicycler-assembly, contributing/create-new-tutorial-content, ecology/ENA_Biodiv_submission, ecology/ref-based-rad-seq, epigenetics/cut_and_run, galaxy-interface/workflow-fairification, genome-annotation/crispr-screen, introduction/galaxy-intro-ngs-data-managment, introduction/vsi_qc, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/mapping, sequence-analysis/quality-control, single-cell/scrna-preprocessing, single-cell/scrna-preprocessing-tenx, transcriptomics/differential-isoform-expression, transcriptomics/full-de-novo, transcriptomics/minerva-pathways, transcriptomics/mirna-target-finder, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts, variant-analysis/exome-seq, variant-analysis/sars-cov-2, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants, variant-analysis/tb-variant-analysis
mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools 2018-06-28 https://github.com/mummer4/mummer 4.0.0 mummer4 4.0.1 To update Sequence Analysis Multiple sequence alignment Multiple sequence alignment Sequence analysis, Human genetics Sequence analysis, Human genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 mummer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 2140 2294 23211 24159 3936 3945 31301 31322 618 618 9228 9228 34 34 388 388 6728 20347 64128 193353 https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef
muon cluster_analyze_embed_muon, mudata_import_export, plot_muon, preprocess_muon muon is a Python framework for multimodal omics analysis 2024-03-15 https://muon.readthedocs.io 0.1.6 muon To update Single Cell, Sequence Analysis, Transcriptomics, Epigenetics Cell biology, Single-cell sequencing, Gene expression, Epigenetics, Multiomics Cell biology, Gene expression, Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/muon/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/muon muon muon muon is a Python framework for multimodal omics analysis. 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mykrobe mykrobe_predict Antibiotic resistance predictions 2017-12-18 https://github.com/Mykrobe-tools/mykrobe 0.10.0 mykrobe 0.13.0 To update Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mzmine_batch mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data 2023-10-21 http://mzmine.github.io/ 3.9.0 mzmine 3.9.0 Up-to-date Metabolomics Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Proteomics, Metabolomics, Proteomics experiment, Small molecules iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 11 11 0 0 0 0 0 0 0 0 0 0 0 0 6 18 11 33
naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) 2022-04-11 https://github.com/BlankenbergLab/nAltORFs 0.1.2 naltorfs 0.1.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 85 228 228 0 0 0 0 0 0 0 0 85 255 228 684
nanocomp nanocomp Compare multiple runs of long read sequencing data and alignments 2025-05-21 https://github.com/wdecoster/NanoComp 1.25.3 nanocomp 1.25.3 Up-to-date Visualization, Statistics, Fastq Manipulation Box-Whisker plot plotting, Visualisation, Multiple sample visualisation Box-Whisker plot plotting, Multiple sample visualisation Nucleic acids, Bioinformatics Nucleic acids, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp nanocomp nanocomp Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. 2020-04-27 https://nanocompore.rna.rocks/ 1.0.0rc3.post2 nanocompore 1.0.4 To update Sequence Analysis Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 12 12 839 839 0 0 0 0 5 5 311 311 0 0 0 0 17 51 1150 3450 https://usegalaxy.eu/published/workflow?id=778923dd04996e07, https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d
nanoplot nanoplot Plotting tool for long read sequencing data and alignments 2018-09-24 https://github.com/wdecoster/NanoPlot 1.44.1 nanoplot 1.44.1 Up-to-date Visualization Scatter plot plotting, Box-Whisker plot plotting Scatter plot plotting, Box-Whisker plot plotting Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 6324 6460 115539 118033 4110 4112 52272 52277 2429 2436 19724 19938 281 281 3680 3680 13144 39577 191215 576358 https://dev.workflowhub.eu/workflows/1005?version=1, https://dev.workflowhub.eu/workflows/1087?version=2, 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nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. 2020-04-27 https://a-slide.github.io/NanopolishComp 0.6.11 nanopolishcomp 0.6.12 To update Sequence Analysis Methylation analysis, Collapsing methods Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation Sequence analysis, Sequencing, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 49 49 1119 1119 0 0 0 0 0 0 0 0 1 1 1 1 50 150 1120 3360 https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d
ncbi_acc_download ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 2019-11-06 https://github.com/kblin/ncbi-acc-download 0.2.8 ncbi-acc-download 0.2.8 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 1869 1892 8944 9040 4848 4873 18770 18827 1072 1072 6704 6704 45 45 329 329 7834 23550 34747 104394 https://dev.workflowhub.eu/workflows/1145?version=1, https://dev.workflowhub.eu/workflows/40?version=1, https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=4d80a87510b2a54e, https://usegalaxy.eu/published/workflow?id=52cb9bacc26b013e, https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://usegalaxy.eu/published/workflow?id=d07fe8b5a045c176, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.fr/published/workflow?id=c7be6e229a045fad, https://usegalaxy.org.au/published/workflow?id=0f71c97671bb401f, https://usegalaxy.org.au/published/workflow?id=cb6f49d4ebfa0891, https://usegalaxy.org.au/published/workflow?id=d62b6717202f42c9, https://usegalaxy.org/published/workflow?id=005924662f68a480, https://usegalaxy.org/published/workflow?id=0596162a499b4074, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://usegalaxy.org/published/workflow?id=2cbcfeb772f348c9, https://usegalaxy.org/published/workflow?id=675d70ee099dd3f2, https://usegalaxy.org/published/workflow?id=be54e57345ce7ca5 genome-annotation/secondary-metabolite-discovery, variant-analysis/baculovirus-isolate-variation
ncbi_datasets datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. 2022-01-27 https://github.com/ncbi/datasets 17.1.0 ncbi-datasets-cli To update Data Source Data handling, Sequence database search, Data retrieval Data handling, Sequence database search, Data retrieval Biological databases Biological databases iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 1259 1259 5354 5354 2847 2847 15172 15172 2 2 3 3 74 74 275 275 4182 12546 20804 62412 https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 genome-annotation/bacterial-comparative-genomics-dataset-construction
ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases 2022-03-22 http://www.ncbi.nlm.nih.gov/books/NBK179288/ 22.4 entrez-direct 24.0 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 3 0 0 0 0 0 0 0 0 0 2 0 3
ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases 2015-04-14 https://www.ncbi.nlm.nih.gov/books/NBK25501/ 1.70 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 2 0 0 0 0 0 0 7 7 0 499 681 2663 3235 0 0 0 0 0 0 0 0 0 0 0 0 499 1679 2663 8561
ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). 2023-09-21 https://github.com/ncbi/fcs-gx 0.5.5 ncbi-fcs-gx 0.5.5 Up-to-date Sequence Analysis Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Sequence analysis, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 624 624 277 277 6095 6095 16 16 51 51 0 0 0 0 358 1074 6770 20310 sequence-analysis/ncbi-fcs
necat necat Error correction and de-novo assembly for ONT Nanopore reads 2021-11-29 https://github.com/xiaochuanle/NECAT 0.0.1_update20200803 necat 0.0.1_update20200803 Up-to-date Assembly De-novo assembly De-novo assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 187 187 975 975 0 0 0 0 0 0 0 0 0 0 0 0 187 561 975 2925
newick_utils newick_display Perform operations on Newick trees 2018-10-01 http://cegg.unige.ch/newick_utils 1.6+galaxy1 newick_utils 1.6 To update Visualization, Metagenomics Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science Phylogeny, Genomics, Computer science iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1290 1387 36948 37965 2039 2039 18100 18100 965 965 8377 8377 47 47 295 295 4341 13120 63720 192177 https://dev.workflowhub.eu/workflows/1077?version=2, https://dev.workflowhub.eu/workflows/1101?version=1, https://dev.workflowhub.eu/workflows/1117?version=1, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=dadca1020f586338, https://usegalaxy.eu/published/workflow?id=dc57118a95b10a80, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=2717e90438c7fb8c, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3, https://usegalaxy.org.au/published/workflow?id=a52609119b30e64d, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=005924662f68a480, https://usegalaxy.org/published/workflow?id=0596162a499b4074, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=6f090b2c259847d2, https://usegalaxy.org/published/workflow?id=775335812a6b7a61, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=d653eaefcf6b4697, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/653?version=1 evolution/abc_intro_phylo, microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short, microbiome/pathogen-detection-from-nanopore-foodborne-data
nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain 2021-03-29 https://github.com/nextstrain/nextclade 2.7.0 nextalign 2.14.0 To update Sequence Analysis Methylation analysis, Variant calling Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics Genomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 0 426 426 4640 4640 291 291 11077 11077 218 218 2235 2235 11 11 669 669 946 2838 18621 55863 https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=5c15f251642bfa1f, https://usegalaxy.eu/published/workflow?id=74f19aff1b9cdd6b, https://usegalaxy.eu/published/workflow?id=9feebfc6c34da287, https://usegalaxy.fr/published/workflow?id=2345fad7dac13daa, https://usegalaxy.fr/published/workflow?id=591c57173e259ca6, https://usegalaxy.fr/published/workflow?id=e4735d214a68b790, https://usegalaxy.fr/published/workflow?id=feb57548b3ce914d, https://usegalaxy.org.au/published/workflow?id=7563b3ef697a69fd, https://usegalaxy.org/published/workflow?id=0fa2ce12c2874b1d, https://usegalaxy.org/published/workflow?id=4b41a8247f52c463, https://usegalaxy.org/published/workflow?id=8b81b9a3b49bbf98, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://workflowhub.eu/workflows/155?version=5, https://workflowhub.eu/workflows/520?version=1 variant-analysis/sars-cov-2-variant-discovery
ngmlr ngmlr CoNvex Gap-cost alignMents for Long Reads 2020-10-27 https://github.com/philres/ngmlr 0.2.7 ngmlr 0.2.7 Up-to-date Next Gen Mappers DNA mapping, Sequence alignment, Genetic variation analysis DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Sequencing, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 51 51 1406 1406 0 0 0 0 0 0 0 0 0 0 0 0 51 153 1406 4218 https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5
ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. 2015-11-10 https://github.com/ngsutils/ngsutils ngsutils 0.5.9 To update SAM Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Read pre-processing, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 685 803 25649 32663 874 1295 16536 23395 126 156 9176 10555 20 20 146 146 1705 5684 51507 169773 https://dev.workflowhub.eu/workflows/1099?version=1, https://dev.workflowhub.eu/workflows/1116?version=1, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=45fc2dada84d251e, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=f33b5135ee99e0dc, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org/published/workflow?id=1f48b44fa22ac5fc, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=71f8a4090877f171, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/102?version=1 assembly/metagenomics-assembly, microbiome/metagenomics-assembly
nonpareil nonpareil Estimate average coverage in metagenomic datasets 2017-11-03 http://nonpareil.readthedocs.io 3.5.5 nonpareil 3.5.5 Up-to-date Metagenomics Operation Operation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 14 16 104 155 21 21 150 150 0 0 0 0 0 0 0 0 35 107 254 813
novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. 2020-05-18 https://github.com/ndierckx/NOVOPlasty 4.3.1 novoplasty 4.3.5 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 404 404 9244 9244 1 1 1 1 115 115 2728 2728 9 9 30 30 529 1587 12003 36009 https://usegalaxy.eu/published/workflow?id=5436eb1c430a38dd
nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. 2016-11-18 https://github.com/tecangenomics/nudup 2.3.3 nudup 2.3.3 Up-to-date SAM, Metagenomics, Sequence Analysis, Transcriptomics Duplication detection, Sequence analysis Duplication detection, Sequence analysis Sequencing, Genomics Sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files 2017-03-22 http://metabarcoding.org/obitools 1.2.13 obitools 1.2.13 Up-to-date Sequence Analysis Sequence analysis, Sequence analysis Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Sequence analysis, DNA, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 1591 1593 40651 40699 0 0 0 0 317 317 4434 4434 51 51 1382 1382 1959 5879 46467 139449 https://dev.workflowhub.eu/workflows/1274?version=2, https://usegalaxy.eu/published/workflow?id=513389e1a8c6bba9, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=edf7e2128f5aef8d, https://usegalaxy.org.au/published/workflow?id=470eb26144325590, https://workflowhub.eu/workflows/655?version=1 ecology/Obitools-metabarcoding
ococo ococo Variant detection of SNVs 2017-12-07 https://github.com/karel-brinda/ococo 0.1.2.6 ococo 0.1.2.7 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 74 93 1830 2008 200 201 1498 1500 0 0 0 0 0 0 0 0 274 842 3328 10164
odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. 2020-04-06 https://github.com/vgteam/odgi 0.3 odgi 0.9.2 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 8 8 29 29 0 0 0 0 0 0 0 0 0 0 0 0 8 24 29 87
omark omark Proteome quality assessment software 2023-11-15 https://github.com/DessimozLab/OMArk 0.3.1 To update Sequence Analysis Sequence assembly validation, Differential protein expression profiling Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability Proteomics, Sequence analysis, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark omark OMArk OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 43 442 442 3 3 3 3 0 0 0 0 4 4 296 296 50 150 741 2223 https://dev.workflowhub.eu/workflows/1358?version=2, https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=7de6e20699183cd3, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.eu/published/workflow?id=9fb31a16b258cc1a, https://workflowhub.eu/workflows/1096?version=2, https://workflowhub.eu/workflows/1255?version=2 genome-annotation/braker3, genome-annotation/helixer
ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. 2020-06-08 https://github.com/nanoporetech/ont_fast5_api/ 3.1.3 ont-fast5-api 4.1.3 To update Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 88 88 3090 3090 0 0 0 0 0 0 0 0 0 0 0 0 88 264 3090 9270 https://usegalaxy.eu/published/workflow?id=d5b1fab611ddfeb0, https://usegalaxy.eu/published/workflow?id=e271d95a671182ec
onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. 2017-11-04 http://search.cpan.org/~easr/ONTO-PERL-1.45/ 1.45 perl-onto-perl 1.45 Up-to-date Ontology Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 0 69 71 443 665 0 0 0 0 0 0 0 0 0 0 0 0 69 209 443 1551
openalex_explorer openalex_explorer Fetch citing papers from OpenAlex using DOI, ID and title 2025-05-29 https://openalex.org/ 0.1.0+galaxy0 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex https://github.com/galaxyproject/tools-iuc/tree/main/tools/openalex 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
optdoe optdoe Optimal Design Of Experiment 2022-10-27 https://github.com/pablocarb/doebase v2.0.2 doebase To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
optitype optitype Precision HLA typing from NGS data 2021-02-17 https://github.com/FRED-2/OptiType 1.3.5 optitype 1.3.5 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 52 52 549 549 6 6 39 39 2 2 39 39 0 0 0 0 60 180 627 1881 https://dev.workflowhub.eu/workflows/1381?version=1, https://usegalaxy.org.au/published/workflow?id=2249ab6710f5e84d, https://usegalaxy.org/published/workflow?id=1d925422fc6094a0 proteomics/neoantigen-6-predicting-hla-binding
orfipy orfipy Galaxy wrapper for ORFIPY 2022-04-07 https://github.com/urmi-21/orfipy 0.0.4 orfipy 0.0.4 Up-to-date Sequence Analysis Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Computer science, RNA-Seq, Transcriptomics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 118 118 1124 1124 280 280 2161 2161 0 0 0 0 0 0 0 0 398 1194 3285 9855 genome-annotation/gene-centric
orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy 2017-05-22 https://github.com/davidemms/OrthoFinder 2.5.5 orthofinder 3.0.1b1 To update Phylogenetics, Sequence Analysis Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 546 546 2570 2570 0 0 0 0 94 94 976 976 33 33 213 213 673 2019 3759 11277
packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection 2022-01-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader 0.1 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pacu pacu_map, pacu_snp PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. 2024-08-13 https://github.com/BioinformaticsPlatformWIV-ISP/PACU 0.0.5 pacu_snp 0.0.7 To update Sequence Analysis, Phylogenetics Clustering Clustering Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 55 55 0 0 0 0 0 0 0 0 0 0 0 0 16 48 55 165
pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing 2024-03-26 https://pairtools.readthedocs.io 1.1.3 pairtools 1.1.3 Up-to-date Sequence Analysis iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 33 365 365 20 20 41 41 0 0 0 0 0 0 0 0 53 159 406 1218 https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1164?version=2
panaroo panaroo A Bacterial Pangenome Analysis Pipeline 2025-02-28 https://gthlab.au/panaroo/#/ 1.5.2 panaroo 1.5.2 Up-to-date Sequence Analysis De-novo assembly, Genome assembly, Clustering De-novo assembly, Genome assembly, Clustering Workflows, Sequence assembly, Gene and protein families, Plant biology, Sequencing Workflows, Sequence assembly, Gene and protein families, Plant biology, Sequencing galaxy-australia https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo panaroo Panaroo Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 129 129 0 0 0 0 16 48 129 387
pangolin pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. 2021-03-06 https://github.com/cov-lineages/pangolin 4.3 pangolin 4.3.1 To update Sequence Analysis Tree-based sequence alignment, Variant classification Tree-based sequence alignment, Variant classification Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 573 573 7622 7622 391 391 8560 8560 268 268 2952 2952 12 12 548 548 1244 3732 19682 59046 https://dev.workflowhub.eu/workflows/1293?version=1, https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=5c15f251642bfa1f, https://usegalaxy.eu/published/workflow?id=74f19aff1b9cdd6b, https://usegalaxy.eu/published/workflow?id=9feebfc6c34da287, https://usegalaxy.fr/published/workflow?id=2345fad7dac13daa, https://usegalaxy.fr/published/workflow?id=591c57173e259ca6, https://usegalaxy.fr/published/workflow?id=e4735d214a68b790, https://usegalaxy.fr/published/workflow?id=feb57548b3ce914d, https://usegalaxy.org.au/published/workflow?id=7563b3ef697a69fd, https://usegalaxy.org/published/workflow?id=0fa2ce12c2874b1d, https://usegalaxy.org/published/workflow?id=4b41a8247f52c463, https://usegalaxy.org/published/workflow?id=8b81b9a3b49bbf98, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://workflowhub.eu/workflows/155?version=5 galaxy-interface/workflow-automation, variant-analysis/sars-cov-2-variant-discovery
parse_mito_blast parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. 2022-05-12 https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py 1.0.2 parse_mito_blast 1.0.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 96 96 426 426 75 75 496 496 24 24 135 135 0 0 0 0 195 585 1057 3171 https://dev.workflowhub.eu/workflows/1359?version=1, https://usegalaxy.eu/published/workflow?id=012762cb4acb068b, https://usegalaxy.eu/published/workflow?id=0f044c9f62773a88, https://usegalaxy.eu/published/workflow?id=12a018217ee146ca, https://usegalaxy.eu/published/workflow?id=2497292e98937a5f, https://usegalaxy.eu/published/workflow?id=2c2f0b4312bae4f4, https://usegalaxy.eu/published/workflow?id=33a052f9a3d5551d, https://usegalaxy.eu/published/workflow?id=3dec7c9b02c3d1ee, https://usegalaxy.eu/published/workflow?id=8d64614d1971065a, https://usegalaxy.eu/published/workflow?id=c4fc3adf8f7ff2bc, https://usegalaxy.org.au/published/workflow?id=0edb9c8b767fa74b, https://usegalaxy.org.au/published/workflow?id=3d47e0de658b3304, https://usegalaxy.org.au/published/workflow?id=5fb44f257e445f56, https://usegalaxy.org.au/published/workflow?id=97e55a900db3863b, https://usegalaxy.org.au/published/workflow?id=c92fead7c30c7497, https://usegalaxy.org.au/published/workflow?id=d2dcd3b54e5082a6, https://usegalaxy.org.au/published/workflow?id=d417e920ff97e4c1, https://usegalaxy.org.au/published/workflow?id=d720c98f7227b6d5, https://usegalaxy.org/published/workflow?id=1b80302437db5937, https://usegalaxy.org/published/workflow?id=5e38c7b36e4918ad, https://usegalaxy.org/published/workflow?id=605160c81d098703, https://usegalaxy.org/published/workflow?id=7c9a55db0b0eb178, https://usegalaxy.org/published/workflow?id=b7fe3873ee5e3a02, https://usegalaxy.org/published/workflow?id=cace9f1359874352, https://usegalaxy.org/published/workflow?id=e887adf3afc3253d, https://usegalaxy.org/published/workflow?id=ea206593698adbfd, https://usegalaxy.org/published/workflow?id=fc2b48600853f3ea, https://workflowhub.eu/workflows/645?version=8 assembly/assembly-decontamination
pathview pathview Pathview is a tool set for pathway based data integration and visualization. 2019-08-26 https://bioconductor.org/packages/release/bioc/html/pathview.html 1.34.0 bioconductor-pathview 1.46.0 To update Statistics, RNA, Micro-array Analysis Pathway or network analysis, Pathway or network visualisation Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1406 1450 7343 7510 1333 1333 7822 7822 203 203 1313 1313 17 17 232 232 2959 8921 16710 50297 https://dev.workflowhub.eu/workflows/1326?version=3, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b transcriptomics/ref-based
pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference 2022-03-10 https://github.com/PacificBiosciences/gcpp 2.0.2 pbgcpp 2.0.2 Up-to-date Variant Analysis Variant calling Variant calling Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. 2022-03-10 https://github.com/PacificBiosciences/pbmm2 1.17.0 pbmm2 1.17.0 Up-to-date Next Gen Mappers Pairwise sequence alignment, Sorting Pairwise sequence alignment, Sorting Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 122 122 0 0 0 0 0 0 0 0 0 0 0 0 28 84 122 366
pe_histogram pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. 2016-06-16 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram 1.0.2 openjdk To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 601 601 6835 6835 932 1046 9075 9900 151 151 867 867 62 62 157 157 1746 5352 16934 51627 https://dev.workflowhub.eu/workflows/1161?version=1, https://dev.workflowhub.eu/workflows/1169?version=2, https://dev.workflowhub.eu/workflows/574?version=1, https://usegalaxy.eu/published/workflow?id=1089e5c66dbcc1a3, https://usegalaxy.eu/published/workflow?id=111527fe542846af, https://usegalaxy.eu/published/workflow?id=1ee43d90b69829e9, https://usegalaxy.eu/published/workflow?id=25aa944237d7fb82, 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https://usegalaxy.org/published/workflow?id=e58a87508a337b91, https://usegalaxy.org/published/workflow?id=e899acc664c8b808, https://usegalaxy.org/published/workflow?id=e9ffad95baa43478, https://usegalaxy.org/published/workflow?id=ea4c2defce2f5258, https://usegalaxy.org/published/workflow?id=eafe4aa62a600e1d, https://usegalaxy.org/published/workflow?id=ee3b8d7ba29da11c, https://usegalaxy.org/published/workflow?id=f0ee8bcd7c8fadca, https://usegalaxy.org/published/workflow?id=fcbe12fc4eaae12e, https://workflowhub.eu/workflows/399?version=19 epigenetics/atac-seq, epigenetics/cut_and_run
peakzilla peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. 2024-02-25 https://github.com/steinmann/peakzilla 1.0 python To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 40 40 0 0 0 0 0 0 0 0 0 0 0 0 13 39 40 120
pear iuc_pear PEAR evaluates all possible paired-end read overlaps 2015-02-11 https://cme.h-its.org/exelixis/web/software/pear/ 0.9.6 pear 0.9.6 Up-to-date Fastq Manipulation Sequence merging Sequence merging Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 312 344 7066 7728 542 1745 6436 21022 201 310 5173 8565 0 0 0 0 1055 4509 18675 74665 https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://workflowhub.eu/workflows/232?version=1
pgxrpi pgx_freqplot, pgx_loader pgxLoader and pgxFreqplot functions from pgxRpi 2025-02-27 https://github.com/progenetix/pgxRpi 1.2.0 bioconductor-pgxrpi 1.2.0 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pgxrpi https://github.com/galaxyproject/tools-iuc/tree/main/tools/pgxRpi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes 2023-02-14 https://github.com/gbouras13/pharokka 1.3.2 \n pharokka\n To update Genome annotation Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 490 490 10645 10645 0 0 0 0 82 82 713 713 0 0 0 0 572 1716 11358 34074
phyloseq phyloseq_add_rank_names, phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_bar, phyloseq_plot_ordination, phyloseq_plot_richness, phyloseq_tax_glom Handling and analysis of high-throughput microbiome census data 2022-03-03 https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html 1.50.0 bioconductor-phyloseq 1.50.0 Up-to-date Metagenomics Deposition, Analysis, Visualisation Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Microbiology, Sequence analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. 4 1 7 6 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 307 307 1879 1879 72 72 284 284 9 9 63 63 13 13 22 22 401 1203 2248 6744 https://dev.workflowhub.eu/workflows/1105?version=2, https://usegalaxy.org/published/workflow?id=4faff660f6defa10 microbiome/dada-16S
phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. 2019-05-27 http://www.atgc-montpellier.fr/phyml/ 3.3.20220408 phyml 3.3.20220408 Up-to-date Phylogenetics Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Phylogenetics, Bioinformatics, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 257 280 2048 2165 0 0 0 0 141 154 551 604 74 74 326 326 472 1452 2925 8945 https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0
picard picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. 2017-01-11 http://broadinstitute.github.io/picard/ 3.1.1 picard 3.4.0 To update SAM Formatting Formatting Sequencing Sequencing devteam 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https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1, https://workflowhub.eu/workflows/353?version=1, https://workflowhub.eu/workflows/357?version=1, https://workflowhub.eu/workflows/35?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/395?version=15, https://workflowhub.eu/workflows/399?version=19 epigenetics/atac-seq, epigenetics/cut_and_run, genome-annotation/funannotate, introduction/galaxy-intro-ngs-data-managment, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts, variant-analysis/non-dip, variant-analysis/sars-cov-2
pick_value pick_value Compose a text parameter value using text, integer and float values 2023-01-23 0.2.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 69 69 3462 3462 100 100 6099 6099 5 5 399 399 0 0 0 0 174 522 9960 29880 https://usegalaxy.eu/published/workflow?id=023a0ee62dd1f593, https://usegalaxy.eu/published/workflow?id=089e5e83b1de0511, https://usegalaxy.eu/published/workflow?id=0c92c3c322c3effe, https://usegalaxy.eu/published/workflow?id=1ac0a15758277730, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2b00b6498a2b4779, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3a3e2d50fe7a9ee3, 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picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers 2016-11-08 https://picrust.github.io/picrust/ 1.1.1 picrust 1.1.4 To update Metagenomics Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. 0 6 5 6 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 134 167 759 1136 0 0 0 0 123 123 2322 2322 60 60 429 429 317 984 3510 10907
picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2021-07-09 https://github.com/picrust/picrust2/wiki 2.5.3 picrust2 2.6.2 To update Metagenomics Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 561 561 3685 3685 1 1 1 1 119 119 1742 1742 0 0 0 0 681 2043 5428 16284 https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34
pilon pilon pilon is a tool for assembly improvement and variant analysis in bacteria 2016-08-11 https://github.com/broadinstitute/pilon/wiki 1.20.1 pilon 1.24 To update Variant Analysis Sequence assembly, Analysis, Read alignment Sequence assembly, Analysis Assembly Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1213 1250 9551 10243 1192 1194 8459 8465 802 825 4174 4533 21 21 111 111 3228 9746 22295 67942 https://dev.workflowhub.eu/workflows/1005?version=1, https://dev.workflowhub.eu/workflows/1139?version=1, https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=3588c40cab9b4e1d, https://usegalaxy.org.au/published/workflow?id=02c74095a7128c9d, https://usegalaxy.org.au/published/workflow?id=22bd45f60c60a338, https://usegalaxy.org.au/published/workflow?id=2cb16d321a804b1a, https://usegalaxy.org.au/published/workflow?id=7c343e5b55474d19, https://usegalaxy.org.au/published/workflow?id=b5403e4fff2961f9, https://usegalaxy.org/published/workflow?id=bff206b4625375bc assembly/chloroplast-assembly
pipelign pipelign Multipe sequence alignment 2019-08-20 https://github.com/asmmhossain/pipelign/ 0.2 pipelign 0.2 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 268 271 1495 1514 694 699 9377 9404 0 0 0 0 0 0 0 0 962 2894 10872 32662
pizzly pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. 2017-09-03 https://github.com/pmelsted/pizzly/ 0.37.3.1 pizzly 0.37.3 To update Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 22 25 200 219 84 84 1729 1729 0 0 0 0 0 0 0 0 106 321 1929 5806
plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. 2018-09-05 https://github.com/smaegol/PlasFlow 1.1.0 plasflow 1.1.0 Up-to-date Sequence Analysis Sequence analysis Sequence analysis Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 805 857 51000 51597 702 704 7425 7427 68 68 3148 3148 0 0 0 0 1575 4779 61573 185318 https://dev.workflowhub.eu/workflows/1107?version=1, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://workflowhub.eu/workflows/406?version=1 microbiome/plasmid-metagenomics-nanopore
plasmidfinder plasmidfinder "PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" 2022-09-19 https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ 2.1.6 plasmidfinder 2.1.6 Up-to-date Sequence Analysis Genome assembly, Scaffolding, Multilocus sequence typing Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Whole genome sequencing, Sequence assembly, Mapping, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 622 622 21867 21867 263 263 2923 2923 99 99 1462 1462 34 34 6370 6370 1018 3054 32622 97866 https://dev.workflowhub.eu/workflows/1136?version=2, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=9 genome-annotation/bacterial-genome-annotation
plink plink Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 2020-09-14 https://www.cog-genomics.org/plink 1.90b6.21 plink 1.90b6.21 Up-to-date Genome-Wide Association Study Genetic variation analysis Genetic variation analysis GWAS study GWAS study iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 142 142 934 934 61 61 867 867 0 0 0 0 6 6 64 64 209 627 1865 5595
polypolish polypolish "Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." 2022-09-22 https://github.com/rrwick/Polypolish 0.6.0 polypolish 0.6.0 Up-to-date Sequence Analysis Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping Sequence assembly, Sequence composition, complexity and repeats, Mapping iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 112 112 890 890 0 0 0 0 9 9 276 276 8 8 76 76 129 387 1242 3726 https://dev.workflowhub.eu/workflows/1178?version=1 assembly/mrsa-nanopore
porechop porechop Porechop - Finding and removing adapters from Oxford Nanopore reads 2018-09-13 https://github.com/rrwick/Porechop porechop 0.2.4 To update Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2984 3110 321684 323742 2411 2414 100549 100553 1194 1199 58191 58998 0 0 0 0 6589 19901 480424 1444141 https://dev.workflowhub.eu/workflows/1064?version=1, https://dev.workflowhub.eu/workflows/1087?version=2, https://dev.workflowhub.eu/workflows/1097?version=1, https://usegalaxy.eu/published/workflow?id=0590554db9794d13, https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c, https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc, https://usegalaxy.eu/published/workflow?id=201e65bcf2b71584, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302, https://usegalaxy.eu/published/workflow?id=346b46e6316c6950, https://usegalaxy.eu/published/workflow?id=4a39d38fde81e35d, https://usegalaxy.eu/published/workflow?id=57d3109f32defa3b, https://usegalaxy.eu/published/workflow?id=70d3ebf31940bfb3, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=889f2782ad82bd69, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b, https://usegalaxy.org.au/published/workflow?id=479c6b0a96ea1610, https://usegalaxy.org.au/published/workflow?id=4c7e0703aace6aa3, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2, https://usegalaxy.org.au/published/workflow?id=803ef29108e36e58, https://usegalaxy.org.au/published/workflow?id=c4d23297f6fbf5f3, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org/published/workflow?id=21161075002d6778, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=5626a440a5798458, https://usegalaxy.org/published/workflow?id=574e42683dc3961b, https://usegalaxy.org/published/workflow?id=60f0d0d5d6e93941, https://usegalaxy.org/published/workflow?id=b7817a12dbee583c, https://usegalaxy.org/published/workflow?id=badd4b56dbdeaba7, https://usegalaxy.org/published/workflow?id=cfa9e6e722b086c8, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1114?version=1 assembly/mrsa-nanopore, microbiome/beer-data-analysis, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data
poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. 2017-12-17 https://poretools.readthedocs.io/en/latest/ 0.6.1a1 poretools 0.6.1a1 Up-to-date Fasta Manipulation, Fastq Manipulation Nucleic acid sequence analysis Nucleic acid sequence analysis DNA, Sequencing DNA, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. 13 13 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 0 968 1280 18931 20989 2026 2666 33599 42577 366 397 9688 10246 0 0 0 0 3360 11063 62218 198248
ppanggolin ppanggolin_all, ppanggolin_msa Microbial Partitioned PanGenome 2025-01-22 https://github.com/labgem/PPanGGOLiN 2.2.3 ppanggolin 2.2.3 Up-to-date Genome annotation Rarefaction, Essential dynamics, Sequence assembly, Genome annotation Rarefaction, Essential dynamics, Sequence assembly, Genome annotation Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin ppanggolin PPanGGOLiN PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 genome-annotation/bacterial-pangenomics
presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. 2017-08-30 https://presto.readthedocs.io/ 0.6.2 presto 0.7.4 To update Sequence Analysis Nucleic acid sequence analysis Nucleic acid sequence analysis Sequencing, DNA, Immunology Sequencing, DNA, Immunology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1562 1793 69942 73477 0 0 0 0 0 0 0 0 1562 4917 69942 213361 https://usegalaxy.org/published/workflow?id=34f3aac3aed0f97a, https://usegalaxy.org/published/workflow?id=51f936d1a4e849fa
prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets 2016-05-30 http://prinseq.sourceforge.net/manual.html @TOOL_VERSION+galaxy2 prinseq 0.20.4 To update Fastq Manipulation, Metagenomics Read pre-processing, Sequence trimming, Sequence contamination filtering Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics Transcriptomics, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 272 319 11812 12556 1398 1408 11519 11567 0 0 0 0 10 10 13 13 1680 5097 23344 70824 https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c, https://usegalaxy.eu/published/workflow?id=f9648091c06171cd, https://workflowhub.eu/workflows/1271?version=1, https://workflowhub.eu/workflows/1272?version=1
prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes 2024-03-14 https://github.com/hyattpd/Prodigal 2.6.3 prodigal 2.6.3 Up-to-date Genome annotation Genome annotation Genome annotation Genomics, Sequence analysis Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 233 233 2484 2484 0 0 0 0 23 23 187 187 12 12 1432 1432 268 804 4103 12309 https://dev.workflowhub.eu/workflows/1357?version=1, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b ecology/marine_omics_bgc
progressivemauve progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner 2015-05-15 http://darlinglab.org/mauve/user-guide/progressivemauve.html progressivemauve snapshot_2015_02_13 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 754 794 2304 2514 1156 1156 3210 3210 0 0 0 0 1 1 1 1 1911 5773 5515 16755
prokka prokka Rapid annotation of prokaryotic genomes 2016-10-07 http://github.com/tseemann/prokka 1.14.6 prokka 1.14.6 Up-to-date Sequence Analysis Gene prediction, Coding region prediction, Genome annotation Coding region prediction, Genome annotation Genomics, Model organisms, Virology Genomics, Model organisms, Virology crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 0 1 1 1 0 8552 8940 525752 544268 12582 14164 377905 404664 4647 5382 163580 178101 340 340 5425 5425 26121 81068 1072662 3277782 https://dev.workflowhub.eu/workflows/1000?version=1, https://dev.workflowhub.eu/workflows/1005?version=1, https://dev.workflowhub.eu/workflows/1139?version=1, https://dev.workflowhub.eu/workflows/1182?version=2, https://dev.workflowhub.eu/workflows/1186?version=2, https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=12653a1e65a20304, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=165089132248a0b0, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a847773b563b2328, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=cf8591391a17a914, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4, https://usegalaxy.eu/published/workflow?id=e8eb80ee09159bac, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=33401b29d277b447, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=39c724282ee008e3, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=6c67e22d18566af3, https://usegalaxy.org.au/published/workflow?id=7c343e5b55474d19, https://usegalaxy.org.au/published/workflow?id=87cdeb05b1ebeab0, https://usegalaxy.org.au/published/workflow?id=8f7d5ebead46a6d0, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=b5403e4fff2961f9, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=e20172eb0f30d6cd, https://usegalaxy.org.au/published/workflow?id=f01be6a7685ac476, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=0795dd1d83662bae, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=b43b72dcf5f7694d, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be assembly/chloroplast-assembly, assembly/unicycler-assembly, genome-annotation/annotation-with-prokka
prot_scriber prot_scriber Protein annotation of short human readable descriptions 2022-05-10 https://github.com/usadellab/prot-scriber 0.1.6 prot-scriber 0.1.6 Up-to-date Proteomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 12 12 0 0 0 0 0 0 0 0 0 0 0 0 8 24 12 36
proteinortho proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. 2020-02-05 https://gitlab.com/paulklemm_PHD/proteinortho 6.3.5 proteinortho 6.3.5 Up-to-date Proteomics Sequence clustering, Sequence analysis Sequence clustering, Sequence analysis Comparative genomics Comparative genomics iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 549 549 4314 4314 0 0 0 0 0 0 0 0 0 0 0 0 549 1647 4314 12942 https://dev.workflowhub.eu/workflows/1264?version=2, https://workflowhub.eu/workflows/358?version=1 ecology/phylogeny-data-prep
psiclass psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. 2023-09-06 https://github.com/splicebox/PsiCLASS 1.0.3 psiclass 1.0.3 Up-to-date Transcriptomics Transcriptome assembly Transcriptome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 26 26 0 0 0 0 0 0 0 0 0 0 0 0 6 18 26 78
pureclip pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data 2018-04-26 https://github.com/skrakau/PureCLIP 1.0.4 pureclip 1.3.1 To update Sequence Analysis, RNA, CLIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 83 97 1298 1559 0 0 0 0 0 0 0 0 0 0 0 0 83 263 1298 4155 https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=8fb156020285e049
purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth 2021-02-03 https://github.com/dfguan/purge_dups 1.2.6 purge_dups 1.2.6 Up-to-date Assembly Genome assembly, Read binning, Scaffolding Genome assembly, Read binning, Scaffolding Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 318 318 18481 18481 80 80 1310 1310 68 68 2531 2531 0 0 0 0 466 1398 22322 66966 https://dev.workflowhub.eu/workflows/1002?version=1, https://dev.workflowhub.eu/workflows/1187?version=2, https://dev.workflowhub.eu/workflows/233?version=1, https://usegalaxy.eu/published/workflow?id=032a7281a86eba0d, https://usegalaxy.eu/published/workflow?id=0444c98a3ca2a3ca, https://usegalaxy.eu/published/workflow?id=0a3ebee985c26060, https://usegalaxy.eu/published/workflow?id=12b0bd336c76a874, https://usegalaxy.eu/published/workflow?id=3192f92ac4d389b8, https://usegalaxy.eu/published/workflow?id=3480204a99bf4a35, https://usegalaxy.eu/published/workflow?id=399048afb4acef3d, https://usegalaxy.eu/published/workflow?id=5bf6718e7d6158d2, https://usegalaxy.eu/published/workflow?id=69be0fb8276753ec, https://usegalaxy.eu/published/workflow?id=6c14b08a7ef7e79a, https://usegalaxy.eu/published/workflow?id=700fa3ab11a8f3e2, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=915ffef5b14c871e, https://usegalaxy.eu/published/workflow?id=9667bf36217083b7, https://usegalaxy.eu/published/workflow?id=a3f082ff30357040, https://usegalaxy.eu/published/workflow?id=aef62f4d0bba003b, https://usegalaxy.eu/published/workflow?id=b5de94e9cde071ab, https://usegalaxy.eu/published/workflow?id=bac84a7033c3423f, https://usegalaxy.eu/published/workflow?id=ca39822372847670, https://usegalaxy.eu/published/workflow?id=d02458f1d7d9c3f4, https://usegalaxy.eu/published/workflow?id=d261bbd05889ce75, https://usegalaxy.eu/published/workflow?id=d67299c34e63f3d9, https://usegalaxy.eu/published/workflow?id=d924fafd8e042952, https://usegalaxy.eu/published/workflow?id=f7cdaf862e6599c0, https://usegalaxy.eu/published/workflow?id=f91245e580319e65, https://usegalaxy.org.au/published/workflow?id=06564b19b0655c19, https://usegalaxy.org.au/published/workflow?id=0810be3d7d2b0322, https://usegalaxy.org.au/published/workflow?id=094655df3ccd0b00, https://usegalaxy.org.au/published/workflow?id=0c11e1ba5e8fa21b, https://usegalaxy.org.au/published/workflow?id=0df25e2dbd5e8ed5, https://usegalaxy.org.au/published/workflow?id=1905ec04d5841f09, https://usegalaxy.org.au/published/workflow?id=1ce2a725df3adb74, https://usegalaxy.org.au/published/workflow?id=1dcc1b25c9091fbf, https://usegalaxy.org.au/published/workflow?id=40740c32b9a550c9, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=4ebf1297793870e7, https://usegalaxy.org.au/published/workflow?id=543fb2d9431a7e13, https://usegalaxy.org.au/published/workflow?id=7168c01be9997823, https://usegalaxy.org.au/published/workflow?id=7909da83448d8bf4, https://usegalaxy.org.au/published/workflow?id=79bf7b0f5e9052d7, https://usegalaxy.org.au/published/workflow?id=82d0876385b5ac60, https://usegalaxy.org.au/published/workflow?id=a1015b83baa0eb6d, https://usegalaxy.org.au/published/workflow?id=a209f43d8a3cc853, https://usegalaxy.org.au/published/workflow?id=ac8bdc5a0b2d70cd, https://usegalaxy.org.au/published/workflow?id=c556c2270200801d, https://usegalaxy.org.au/published/workflow?id=d83d5ecf31c20490, https://usegalaxy.org.au/published/workflow?id=e5dfeff4a3068f36, https://usegalaxy.org.au/published/workflow?id=ecfb8a08e5a40e15, https://usegalaxy.org.au/published/workflow?id=f895914e322c8b77, https://usegalaxy.org.au/published/workflow?id=fea0e6c02c2f6274, https://usegalaxy.org/published/workflow?id=242ef2e9dee35702, https://usegalaxy.org/published/workflow?id=3753dcca4100e976, https://usegalaxy.org/published/workflow?id=426358bd988cb39d, https://usegalaxy.org/published/workflow?id=45c0b677c4920d03, https://usegalaxy.org/published/workflow?id=49c9e8161a46667f, https://usegalaxy.org/published/workflow?id=5edabfc62f58d8cf, https://usegalaxy.org/published/workflow?id=6fc7497c86ebd8ee, https://usegalaxy.org/published/workflow?id=7adf904dea83e699, https://usegalaxy.org/published/workflow?id=8ccb42012dcb5db2, https://usegalaxy.org/published/workflow?id=96bd0007dceec123, https://usegalaxy.org/published/workflow?id=9ab68c65337b893b, https://usegalaxy.org/published/workflow?id=c09b8a0c96123cbb, https://usegalaxy.org/published/workflow?id=cb4ccd3068819418, https://usegalaxy.org/published/workflow?id=cc50da71cdf6f244, https://usegalaxy.org/published/workflow?id=d2e8a6b39fe88f4c, https://usegalaxy.org/published/workflow?id=eaf96fa3c39c210b, https://workflowhub.eu/workflows/1163?version=1, https://workflowhub.eu/workflows/237?version=2, https://workflowhub.eu/workflows/606?version=2, https://workflowhub.eu/workflows/633?version=15, https://workflowhub.eu/workflows/701?version=1, https://workflowhub.eu/workflows/751?version=9 assembly/vgp_genome_assembly
pycoqc pycoqc QC metrics for ONT Basecalling 2021-03-02 https://github.com/tleonardi/pycoQC 2.5.2 pycoqc 2.5.2 Up-to-date Nanopore Sequencing quality control, Statistical calculation Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Sequence analysis, Data quality management, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 665 665 23072 23072 911 911 2798 2798 486 486 946 946 146 146 292 292 2208 6624 27108 81324 https://usegalaxy.org.au/published/workflow?id=01393562b82f1884, https://usegalaxy.org.au/published/workflow?id=0d1d4392c3042fbd, https://usegalaxy.org.au/published/workflow?id=31dbe7344d72b903, https://usegalaxy.org.au/published/workflow?id=364025bd13970867, https://usegalaxy.org.au/published/workflow?id=419e09e4a2fa6d38, https://usegalaxy.org.au/published/workflow?id=5f4e164c18810cca, https://usegalaxy.org.au/published/workflow?id=866b69c5ee6601fe, https://usegalaxy.org.au/published/workflow?id=8fe84de499e96485, https://usegalaxy.org.au/published/workflow?id=c87b645aedfb857d, https://usegalaxy.org.au/published/workflow?id=da3d4b39b0d655e7, https://usegalaxy.org.au/published/workflow?id=ed43af416c6a7d3b, https://usegalaxy.org.au/published/workflow?id=fdf32312e8567093 sequence-analysis/quality-control
pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. 2018-06-08 https://github.com/deeptools/pyGenomeTracks 3.8 pygenometracks 3.9 To update Visualization Visualisation, Formatting Visualisation, Formatting Model organisms, Imaging, Workflows Model organisms, Imaging, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1147 1191 13678 14617 1204 1204 9770 9770 155 155 4012 4012 31 31 62 62 2537 7655 27522 83505 https://dev.workflowhub.eu/workflows/1161?version=1, https://dev.workflowhub.eu/workflows/1169?version=2, https://dev.workflowhub.eu/workflows/1324?version=3, https://dev.workflowhub.eu/workflows/1329?version=5, https://usegalaxy.eu/published/workflow?id=02655d0e4af0ee0d, https://usegalaxy.eu/published/workflow?id=2a9c812f59b7b36c, https://usegalaxy.eu/published/workflow?id=4464d3b0fc782a1a, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=506a451679fe25b4, https://usegalaxy.eu/published/workflow?id=72201ffaf488f278, https://usegalaxy.eu/published/workflow?id=9843ae66c3b367b7, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9f8a93cfffb31cd6, https://usegalaxy.eu/published/workflow?id=9fc8b89954c04ee1, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=f394d1b12779ba41, https://usegalaxy.org.au/published/workflow?id=13ce18408ee7acc9, https://usegalaxy.org.au/published/workflow?id=99821674db7682bb, https://usegalaxy.org/published/workflow?id=06eaa5b141fe7a08, https://usegalaxy.org/published/workflow?id=0bc1b8888d8b20c4, https://usegalaxy.org/published/workflow?id=1dc312e3fba9f810, https://usegalaxy.org/published/workflow?id=4998f171ec922c7d, https://usegalaxy.org/published/workflow?id=582f3de3971fc38c, https://usegalaxy.org/published/workflow?id=7353afb9301780e5, https://usegalaxy.org/published/workflow?id=b31ab9e76409a9b7, https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://usegalaxy.org/published/workflow?id=f13432eef7ac28e9, https://usegalaxy.org/published/workflow?id=f80b80aa7fb196ba, https://workflowhub.eu/workflows/420?version=3 epigenetics/atac-seq, transcriptomics/differential-isoform-expression, transcriptomics/ref-based
pysradb_search pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. 2022-11-10 https://github.com/saketkc/pysradb 1.4.2 pysradb 2.2.2 To update Sequence Analysis Deposition, Data retrieval Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics Sequencing, Gene transcripts, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 42 42 175 175 0 0 0 0 0 0 0 0 0 0 0 0 42 126 175 525
qfilt qfilt Filter sequencing data 2018-06-06 https://github.com/veg/qfilt 1.0.0+galaxy1 qfilt 0.0.1 To update Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
qiime qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis 2017-01-16 http://www.qiime.org qiime 1.9.1 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 32 32 0 0 0 0 0 0 0 0 0 0 0 31 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 3528 4113 33828 38321 2 2 1617 1617 5 5 16 16 178 180 4475 4479 3713 11726 39936 124305 https://dev.workflowhub.eu/workflows/1287?version=2, https://dev.workflowhub.eu/workflows/1292?version=2, https://usegalaxy.eu/published/workflow?id=3acfb87be6db2303, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a sequence-analysis/Manage_AB1_Sanger
qiime qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis 2017-01-16 http://www.qiime.org qiime 1.9.1 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 206 250 2109 2460 0 0 0 0 1 1 2 2 7 7 13 13 214 686 2124 6723 https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4
qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts 2022-10-06 http://www.qiime.org 0.1.0 unzip To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 104 104 0 0 0 0 0 0 0 0 0 0 0 0 17 51 104 312 https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34
qq_tools qq_manhattan 2020-10-07 https://CRAN.R-project.org/package=qqman 0.1.0 r-qqman 0.1.4 To update Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 16 16 1 3 16 48
qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. 2019-10-10 http://qualimap.bioinfo.cipf.es/ 2.3 qualimap 2.3 Up-to-date Sequence Analysis, Transcriptomics, SAM Sequencing quality control Sequencing quality control Data quality management Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 0 0 0 0 1 0 0 0 0 0 4 4 4 0 3427 3520 703635 704758 4439 4450 109291 109374 876 876 37544 37544 48 48 6750 6750 8790 26474 857220 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https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/110?version=10, https://workflowhub.eu/workflows/111?version=5, https://workflowhub.eu/workflows/1260?version=1, https://workflowhub.eu/workflows/155?version=5, https://workflowhub.eu/workflows/439?version=2, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/628?version=1 variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon, variant-analysis/tb-variant-analysis
quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. 2016-09-07 http://quast.bioinf.spbau.ru/ 5.3.0 quast 5.3.0 Up-to-date Assembly Visualisation, Sequence assembly validation Visualisation, Sequence assembly validation Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 8965 9298 91117 94741 11073 12385 66080 72394 4262 4551 38178 40828 463 465 8175 8213 24763 76225 203550 623276 https://dev.workflowhub.eu/workflows/1000?version=1, https://dev.workflowhub.eu/workflows/1002?version=1, https://dev.workflowhub.eu/workflows/1003?version=1, https://dev.workflowhub.eu/workflows/1004?version=1, https://dev.workflowhub.eu/workflows/1006?version=1, https://dev.workflowhub.eu/workflows/1103?version=1, https://dev.workflowhub.eu/workflows/1120?version=1, https://dev.workflowhub.eu/workflows/1128?version=1, https://dev.workflowhub.eu/workflows/1131?version=2, https://dev.workflowhub.eu/workflows/1135?version=2, https://dev.workflowhub.eu/workflows/1158?version=2, https://dev.workflowhub.eu/workflows/1170?version=2, https://dev.workflowhub.eu/workflows/1178?version=1, 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https://usegalaxy.org/published/workflow?id=c30f6ca171896908, https://usegalaxy.org/published/workflow?id=c454c930ccfb0d3f, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=c8d74054c1820087, https://usegalaxy.org/published/workflow?id=db08887d7d6dc147, https://usegalaxy.org/published/workflow?id=e745c45651d829b8, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://usegalaxy.org/published/workflow?id=f926e70bee242785, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://workflowhub.eu/workflows/1043?version=7, https://workflowhub.eu/workflows/225?version=1, https://workflowhub.eu/workflows/229?version=1, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/750?version=2, https://workflowhub.eu/workflows/794?version=2 assembly/assembly-quality-control, assembly/general-introduction, assembly/hifi-assembly, assembly/largegenome, assembly/metagenomics-assembly, assembly/mrsa-illumina, assembly/mrsa-nanopore, assembly/unicycler-assembly, assembly/vgp_genome_assembly, assembly/vgp_workflow_training, microbiome/metagenomics-assembly
query_impc query_impc Contains a tool to query the IMPC database. 2023-10-11 https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc 0.9.0 requests To update Convert Formats, Web Services iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 4 4 0 0 0 0 0 0 0 0 0 0 0 0 2 6 4 12
query_tabular filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output 2017-07-14 https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular 3.3.1 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3 3 3 1 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 1 0 0 0 0 0 3 3 3 0 1409 1464 144055 149950 1037 1037 12015 12015 184 184 6783 6783 5 5 6 6 2635 7960 162859 494472 https://dev.workflowhub.eu/workflows/1036?version=1, https://dev.workflowhub.eu/workflows/1041?version=1, https://dev.workflowhub.eu/workflows/1042?version=1, https://dev.workflowhub.eu/workflows/1043?version=1, https://dev.workflowhub.eu/workflows/1099?version=1, https://dev.workflowhub.eu/workflows/1116?version=1, https://dev.workflowhub.eu/workflows/1151?version=2, 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microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/metagenomics-assembly, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/metaproteomics, proteomics/metaquantome-data-creation, proteomics/neoantigen-1-fusion-database-generation, proteomics/neoantigen-2-non-reference-database-generation, proteomics/neoantigen-3-fragpipe-discovery, proteomics/neoantigen-4-peptide-verification, proteomics/neoantigen-5-variant-annotation, proteomics/neoantigen-6-predicting-hla-binding, proteomics/neoantigen-7-hla-binding-novel-peptides, proteomics/proteogenomics-dbcreation, proteomics/proteogenomics-dbsearch, proteomics/proteogenomics-novel-peptide-analysis, transcriptomics/rna-interactome
quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity 2022-07-08 https://github.com/mahulchak/quickmerge 0.3 quickmerge 0.3 Up-to-date Assembly Genome assembly, Scaffolding, De-novo assembly, Genotyping Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
quicktree quicktree neighbour-joining phylogenetic inference 2024-11-21 https://github.com/khowe/quicktree 2.5 quicktree 2.5 Up-to-date Phylogenetics Phylogenetic inference (from molecular sequences) Phylogenetic inference (from molecular sequences) Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree quicktree QuickTree QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 65 65 0 0 0 0 0 0 0 0 0 0 0 0 7 21 65 195 sequence-analysis/tapscan-streptophyte-algae
raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis 2018-03-03 https://github.com/dgrun/RaceID3_StemID2_package/ 0.2.3 r-raceid 0.1.3 To update Single Cell, Transcriptomics Expression profile clustering, Expression analysis, Molecular dynamics Expression profile clustering, Expression analysis, Molecular dynamics Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid RaceID RaceID Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 331 521 1935 4600 1140 1140 2954 2954 19 19 2428 2428 1 1 1 1 1491 4663 7318 24619 https://dev.workflowhub.eu/workflows/1205?version=1, https://dev.workflowhub.eu/workflows/1376?version=1, https://usegalaxy.eu/published/workflow?id=2f8d9fb85242eca7, https://usegalaxy.org.au/published/workflow?id=9dfa217eae285c30 single-cell/scrna-raceid
ragtag ragtag Reference-guided scaffolding of draft genomes tool. 2021-11-10 https://github.com/malonge/RagTag 2.1.0 ragtag 2.1.0 Up-to-date Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 561 561 5401 5401 0 0 0 0 35 35 548 548 23 23 312 312 619 1857 6261 18783 https://usegalaxy.org.au/published/workflow?id=7f37c5366bce5489
rapidnj rapidnj Galaxy wrapper for the RapidNJ tool 2020-05-11 https://birc.au.dk/software/rapidnj/ 2.3.2 rapidnj 2.3.2 Up-to-date Phylogenetics Phylogenetic tree generation Phylogeny Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 2929 2929 280 280 2040 2040 22 22 88 88 12 12 43 43 353 1059 5100 15300 https://dev.workflowhub.eu/workflows/1173?version=2, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.org/published/workflow?id=005924662f68a480, https://usegalaxy.org/published/workflow?id=0596162a499b4074, https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13 genome-annotation/gene-centric
rasusa rasusa Randomly subsample sequencing reads to a specified coverage 2024-02-16 https://github.com/mbhall88/rasusa 2.0.0 rasusa 2.1.0 To update Sequence Analysis Sequence assembly validation, Sequencing quality control Sequence assembly validation Genomics, Sequence analysis, Sequence assembly, Sequencing, RNA-Seq Genomics, Sequence analysis, Sequence assembly, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa rasusa rasusa Rasusa: Randomly subsample sequencing reads to aspecified coverageProduces an unbiased subsample of your reads 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 71 71 0 0 0 0 0 0 0 0 0 0 0 0 13 39 71 213
raven raven Raven is a de novo genome assembler for long uncorrected reads. 2020-11-04 https://github.com/lbcb-sci/raven 1.8.3 raven-assembler 1.8.3 Up-to-date Assembly De-novo assembly, Genome assembly, Read pre-processing De-novo assembly, Genome assembly, Read pre-processing Sequence assembly, Whole genome sequencing, Genomics Sequence assembly, Whole genome sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven raven Raven a de novo genome assembler for long reads.Raven is a de novo genome assembler for long uncorrected reads. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 494 494 10707 10707 0 0 0 0 209 209 12603 12603 20 20 192 192 723 2169 23502 70506
raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference 2015-11-05 http://www.exelixis-lab.org/web/software/raxml/ 8.2.12 raxml 8.2.13 To update Phylogenetics Sequence analysis, Phylogenetic tree analysis Sequence analysis Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1139 1139 13457 13457 759 759 10784 10800 740 933 5201 6560 14 14 222 222 2652 8149 29664 90367 https://dev.workflowhub.eu/workflows/1007?version=1, https://dev.workflowhub.eu/workflows/1300?version=2, https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55 evolution/mtb_phylogeny
rcorrector rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. 2018-05-02 https://github.com/mourisl/Rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 To update Fastq Manipulation Sequencing error detection Sequencing error detection RNA, RNA-Seq, Sequencing RNA, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 64 64 779 779 0 0 0 0 0 0 0 0 0 0 0 0 64 192 779 2337
read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads 2022-01-28 https://github.com/GenomePathogenAnalysisService/read-it-and-keep 0.2.2 read-it-and-keep 0.3.0 To update Sequence Analysis Filtering, Genome alignment Filtering, Genome alignment Pathology, Genomics Pathology, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep read_it_and_keep read_it_and_keep Read-it-and-keep is a bioinformatics tool designed to filter and extract sequencing reads according to user-defined criteria, such as the presence of specific motifs or coverage of regions of interest. This type of filtering can be particularly useful for targeted analyses, where only relevant sequences are retained for further study, optimising computing and storage resources. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 3777 3777 7 7 8 8 0 0 0 0 0 0 0 0 88 264 3785 11355 https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/521?version=1
recentrifuge recentrifuge "With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." 2022-05-04 https://github.com/khyox/recentrifuge 1.16.1 recentrifuge 1.16.1 Up-to-date Metagenomics Taxonomic classification, Expression analysis, Cross-assembly Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Metagenomics, Microbial ecology, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 187 187 792 792 100 100 259 259 23 23 52 52 20 20 1374 1374 330 990 2477 7431 https://dev.workflowhub.eu/workflows/1217?version=2, https://dev.workflowhub.eu/workflows/1344?version=1, https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502, https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88, https://usegalaxy.eu/published/workflow?id=0c47571d20535426, https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=47e14222073e7192, https://usegalaxy.eu/published/workflow?id=884a4415b669690c, https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75, https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962, https://usegalaxy.eu/published/workflow?id=ebb131f2a6172081, https://usegalaxy.fr/published/workflow?id=3d3b40398d1cd1ae, https://usegalaxy.org/published/workflow?id=1be5c982c2d36a6c, https://usegalaxy.org/published/workflow?id=623fc80c7f91a33a, https://usegalaxy.org/published/workflow?id=9f68718f025bed30, https://usegalaxy.org/published/workflow?id=b6a795834009ce06, https://workflowhub.eu/workflows/1052?version=8 ecology/bacterial-isolate-species-contamination-checking, sequence-analysis/quality-contamination-control
red red Red (REpeat Detector) 2022-09-14 https://github.com/BioinformaticsToolsmith/Red 2018.09.10 red 2018.09.10 Up-to-date Sequence Analysis RNA-Seq analysis, Editing RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation RNA, Sequencing, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 1008 1008 230 230 478 478 73 73 294 294 44 44 147 147 609 1827 1927 5781 https://dev.workflowhub.eu/workflows/1198?version=1, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=7de6e20699183cd3, https://usegalaxy.eu/published/workflow?id=9fb31a16b258cc1a, https://usegalaxy.fr/published/workflow?id=55be36ab73515e65, https://workflowhub.eu/workflows/753?version=1 genome-annotation/repeatmasker
repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. 2018-04-21 http://www.repeatmasker.org/ 4.1.5 repeatmasker 4.1.9 To update Sequence Analysis Genome annotation Genome annotation Sequence analysis, Sequence composition, complexity and repeats Sequence composition, complexity and repeats bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1028 1029 7954 7965 993 993 9105 9105 352 352 3810 3810 85 85 518 518 2458 7375 21387 64172 https://dev.workflowhub.eu/workflows/1198?version=1, https://dev.workflowhub.eu/workflows/1264?version=2, https://usegalaxy.eu/published/workflow?id=09c534f738426a6d, https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a71349ba0bff403a, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=ffb1117077f68a9f, https://usegalaxy.org/published/workflow?id=effc17e170263ae6, https://usegalaxy.org/published/workflow?id=f2f633d2b02b6050, https://usegalaxy.org/published/workflow?id=fb8b997f516288e1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/575?version=1, https://workflowhub.eu/workflows/753?version=1, https://workflowhub.eu/workflows/875?version=3 ecology/phylogeny-data-prep, genome-annotation/repeatmasker
repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA 2021-08-26 https://www.repeatmasker.org/RepeatModeler/ 2.0.5 To update Genome annotation Repeat sequence detection Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats Sequence composition, complexity and repeats, Sequence composition, complexity and repeats csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 532 532 8421 8421 297 297 1914 1914 199 199 8739 8739 23 23 249 249 1051 3153 19323 57969 https://usegalaxy.eu/published/workflow?id=09c534f738426a6d, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a71349ba0bff403a, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=ffb1117077f68a9f, https://usegalaxy.org/published/workflow?id=effc17e170263ae6, https://workflowhub.eu/workflows/575?version=1, https://workflowhub.eu/workflows/875?version=3 genome-annotation/repeatmasker
repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. 2015-12-18 matplotlib To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 116 220 354 722 0 0 0 0 0 0 0 0 116 452 354 1430
reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast 2017-05-26 https://cran.r-project.org/web/packages/reshape2/index.html 1.4.2 r-reshape2 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 107 113 3510 3621 168 168 552 553 0 0 0 0 3 3 5 5 278 840 4067 12313 https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://workflowhub.eu/workflows/1189?version=2
resize_coordinate_window resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. 2016-01-13 1.0.2 python To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 9 58 86 23 58 89 217 0 0 0 0 0 0 0 0 30 127 147 597 https://usegalaxy.eu/published/workflow?id=6bce1d419a179c50, https://usegalaxy.org/published/workflow?id=7643e66a9b4e9c11
revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers 2024-03-19 https://gitlab.com/Bernt/revoluzer/ 0.1.8 revoluzer 0.1.8 Up-to-date Phylogenetics Structural variation detection Structural variation detection Molecular evolution, Phylogeny Molecular evolution, Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 78 78 3046 3046 0 0 0 0 0 0 0 0 0 0 0 0 78 234 3046 9138
rgcca rgcca multi-block analysis 2020-09-02 https://github.com/rgcca-factory/RGCCA 3.0.2 rgccacmd 3.0.3 To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 46 46 36 36 85 85 0 0 0 0 0 0 0 0 43 129 131 393
rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper 2015-05-18 https://github.com/alexdobin/STAR 2.7.11b star 2.7.11b Up-to-date Next Gen Mappers, Transcriptomics, Single Cell Sequence alignment Sequence alignment RNA-Seq, Transcriptomics RNA-Seq, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar star STAR Ultrafast universal RNA-seq data aligner 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 2 0 0 0 0 1 2 2 2 0 11087 12172 459789 504479 16286 20665 360596 455052 1438 1568 53075 57044 957 957 9772 9772 29768 94898 883232 2792811 https://dev.workflowhub.eu/workflows/1022?version=1, https://dev.workflowhub.eu/workflows/1202?version=1, https://dev.workflowhub.eu/workflows/1214?version=1, https://dev.workflowhub.eu/workflows/1220?version=3, https://dev.workflowhub.eu/workflows/1285?version=2, 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https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://usegalaxy.org/published/workflow?id=e55ca98817c1855e, https://usegalaxy.org/published/workflow?id=f3c8093c5b8a7233, https://workflowhub.eu/workflows/400?version=12, https://workflowhub.eu/workflows/401?version=13, https://workflowhub.eu/workflows/513?version=3, https://workflowhub.eu/workflows/754?version=1 genome-annotation/braker3, genome-annotation/funannotate, proteomics/neoantigen-1-fusion-database-generation, single-cell/scrna-preprocessing, single-cell/scrna-preprocessing-tenx, transcriptomics/clipseq, transcriptomics/differential-isoform-expression, transcriptomics/ref-based
ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data 2022-09-22 https://github.com/LabTranslationalArchitectomics/riboWaltz 1.2.0 ribowaltz 2.0 To update Transcriptomics, RNA Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 22 22 194 194 0 0 0 0 0 0 0 0 0 0 0 0 22 66 194 582
rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. 2020-10-05 https://github.com/ablab/rnaquast 2.3.0 rnaquast 2.3.0 Up-to-date Assembly, RNA De-novo assembly, Transcriptome assembly, Sequence assembly validation De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-Seq Sequence assembly, Transcriptomics, RNA-Seq iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 285 285 1626 1626 124 124 562 562 8 8 128 128 8 8 100 100 425 1275 2416 7248 https://dev.workflowhub.eu/workflows/1324?version=3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b transcriptomics/differential-isoform-expression
roary roary Roary the pangenome pipeline 2017-06-21 https://sanger-pathogens.github.io/Roary/ 3.13.0 roary 3.13.0 Up-to-date Sequence Analysis Genome assembly Genome assembly DNA, Genomics, Mapping DNA, Genomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1728 1804 16888 18042 2070 2070 14013 14013 573 626 5106 6163 41 41 139 139 4412 13365 36146 110649 https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0
rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output 2023-01-05 https://github.com/brsynth/rp2biosensor 3.2.1 rp2biosensor To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 2022-10-17 https://github.com/brsynth/rp2paths 1.5.1 rp2paths To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://dev.workflowhub.eu/workflows/1142?version=2 synthetic-biology/retrosynthesis_analysis
rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files 2022-03-30 https://github.com/brsynth/rpbasicdesign 1.2.2 rpbasicdesign To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://dev.workflowhub.eu/workflows/1147?version=2 synthetic-biology/basic_assembly_analysis
rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways 2022-01-17 https://github.com/brsynth/rptools/releases 5.12.3 rptools To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://dev.workflowhub.eu/workflows/1048?version=1, https://dev.workflowhub.eu/workflows/1137?version=2 synthetic-biology/pathway_analysis
rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format 2022-11-16 https://github.com/brsynth/rptools 5.13.1 rptools To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rrparser rrparser Reaction Rules Parser 2022-06-27 https://github.com/brsynth/RRParser 2.7.0 rrparser To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://dev.workflowhub.eu/workflows/1142?version=2 synthetic-biology/retrosynthesis_analysis
rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package 2017-02-27 https://code.google.com/p/rseqc/ 5.0.3 rseqc 5.0.4 To update Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization Data handling Data handling Sequencing Sequencing nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. 22 22 22 22 0 0 0 0 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 0 22 0 0 0 0 0 22 22 22 0 9037 10464 149222 164718 11267 14066 141933 179278 1871 1999 26252 28021 1496 1496 43650 43650 23671 75367 361057 1137781 https://dev.workflowhub.eu/workflows/1001?version=1, https://dev.workflowhub.eu/workflows/1295?version=1, https://dev.workflowhub.eu/workflows/1299?version=2, https://dev.workflowhub.eu/workflows/1324?version=3, https://dev.workflowhub.eu/workflows/1327?version=1, https://dev.workflowhub.eu/workflows/1329?version=5, https://usegalaxy.eu/published/workflow?id=1ee43d90b69829e9, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=5e4135eeb4972709, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=a52c5dd688def9ba, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.eu/published/workflow?id=cc37667c2d1f9056, https://usegalaxy.eu/published/workflow?id=ccef778cfd9024d1, https://usegalaxy.eu/published/workflow?id=f33b5135ee99e0dc, https://usegalaxy.fr/published/workflow?id=334189184455d9a2, https://usegalaxy.fr/published/workflow?id=5d83e0886f2a7465, https://usegalaxy.fr/published/workflow?id=74b4d11c07f7f0a4, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=85aede91db0122e4, https://usegalaxy.org.au/published/workflow?id=a763e53653b10ce0, https://usegalaxy.org.au/published/workflow?id=af7b95f46485308c, https://usegalaxy.org.au/published/workflow?id=b08342866a118a5e, https://usegalaxy.org.au/published/workflow?id=bb0feff5d764df60, https://usegalaxy.org.au/published/workflow?id=ce7f6a1c824920e2, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=044c5ce43f2e1829, https://usegalaxy.org/published/workflow?id=57165345b898b978, https://usegalaxy.org/published/workflow?id=582f3de3971fc38c, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=7022c4d9af725e5c, https://usegalaxy.org/published/workflow?id=73f5b1a6fd3c703f, https://usegalaxy.org/published/workflow?id=76b8ed1c68678b62, https://usegalaxy.org/published/workflow?id=7e9269e78e989480, https://usegalaxy.org/published/workflow?id=a743746151101352, https://usegalaxy.org/published/workflow?id=b11796364c22235e, https://usegalaxy.org/published/workflow?id=b1a98a2d5ebda1c5, https://usegalaxy.org/published/workflow?id=e035be74e3c85bf5, https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/688?version=1 transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts
ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data 2018-08-30 https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html 1.26.0 bioconductor-ruvseq 1.40.0 To update Transcriptomics, RNA, Statistics Differential gene expression analysis Differential gene expression analysis Gene expression, RNA-seq Gene expression iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 169 197 1261 1412 313 313 2325 2325 0 0 0 0 0 0 0 0 482 1474 3586 10909
salsa salsa A tool to scaffold long read assemblies with Hi-C 2021-01-14 https://github.com/marbl/SALSA 2.3 salsa2 2.3 Up-to-date Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Sequence assembly, DNA binding sites, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 122 122 467 467 94 94 1057 1057 24 24 410 410 0 0 0 0 240 720 1934 5802 https://dev.workflowhub.eu/workflows/1002?version=1, https://dev.workflowhub.eu/workflows/1187?version=2, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467 assembly/vgp_genome_assembly
samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files 2016-12-18 https://github.com/GregoryFaust/samblaster 0.1.26 samblaster 0.1.26 Up-to-date SAM, Fastq Manipulation, Variant Analysis Split read mapping Split read mapping DNA, Sequencing, Mapping DNA, Sequencing, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
samtools 2017-01-24 https://github.com/samtools/samtools 1.20 samtools 1.22 To update SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sansa sansa_annotate Sansa is a tool for structural variant annotation. 2020-12-05 https://github.com/dellytools/sansa 0.2.2 sansa 0.2.3 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 36 36 139 139 0 0 0 0 0 0 0 0 0 0 0 0 36 108 139 417
sarscov2formatter sarscov2formatter sarscov2formatter custom script 2020-05-01 https://github.com/nickeener/sarscov2formatter 1.0 sarscov2formatter 1.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 16 16 174 174 30 30 400 400 0 0 0 0 0 0 0 0 46 138 574 1722 https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e
sarscov2summary sarscov2summary sarscov2summary custom script 2020-05-01 https://github.com/nickeener/sarscov2summary 0.1 sarscov2summary 0.5 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5 5 140 140 6 6 253 253 0 0 0 0 0 0 0 0 11 33 393 1179 https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e
sbml2sbol sbml2sbol Convert SBML to SBOL format 2022-10-15 https://github.com/neilswainston/SbmlToSbol 0.1.13 sbml2sbol To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python 2019-03-04 https://scanpy.readthedocs.io 1.10.2 scanpy 1.7.2 To update Single Cell, Spatial Omics, Transcriptomics Differential gene expression analysis Differential gene expression analysis Gene expression, Cell biology, Genetics, Single-cell sequencing Gene expression, Cell biology, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 2684 2739 68358 69738 1350 1350 33577 33577 413 413 20077 20077 0 0 0 0 4447 13396 122012 367416 https://dev.workflowhub.eu/workflows/1011?version=1, https://dev.workflowhub.eu/workflows/1013?version=1, https://dev.workflowhub.eu/workflows/1014?version=1, https://dev.workflowhub.eu/workflows/1016?version=1, https://dev.workflowhub.eu/workflows/1017?version=1, https://dev.workflowhub.eu/workflows/1212?version=1, https://dev.workflowhub.eu/workflows/1219?version=2, https://dev.workflowhub.eu/workflows/1246?version=2, https://dev.workflowhub.eu/workflows/1259?version=3, https://dev.workflowhub.eu/workflows/1266?version=1, https://dev.workflowhub.eu/workflows/1275?version=1, https://dev.workflowhub.eu/workflows/1343?version=2, https://dev.workflowhub.eu/workflows/1377?version=1, https://dev.workflowhub.eu/workflows/1378?version=1, https://usegalaxy.eu/published/workflow?id=0d7c643d7720ee31, https://usegalaxy.eu/published/workflow?id=171d6fca2c3339e2, https://usegalaxy.eu/published/workflow?id=21315ffd2df2f159, https://usegalaxy.eu/published/workflow?id=37e51e215684bdcc, https://usegalaxy.eu/published/workflow?id=715ca378c1d68de3, https://usegalaxy.eu/published/workflow?id=77e85bde57477194, https://usegalaxy.eu/published/workflow?id=78dc6fca5b58ec05, https://usegalaxy.eu/published/workflow?id=8ce45d9ca1b62624, https://usegalaxy.eu/published/workflow?id=921cab3e6faf30be, https://usegalaxy.eu/published/workflow?id=9a7d8552f5774fbd, https://usegalaxy.eu/published/workflow?id=ae79275d3568ad31, https://usegalaxy.eu/published/workflow?id=b3cf397fd4d1bea8, https://usegalaxy.eu/published/workflow?id=b5627201bb4f6943, https://usegalaxy.eu/published/workflow?id=d70dc4cfeedb690b, https://usegalaxy.eu/published/workflow?id=d7c0c972c471d514, https://usegalaxy.eu/published/workflow?id=ddced7b107e4707a, https://usegalaxy.eu/published/workflow?id=e2391c40d24d403f, https://usegalaxy.eu/published/workflow?id=e472096116cbe392, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://usegalaxy.eu/published/workflow?id=f05754467a439134, https://usegalaxy.org.au/published/workflow?id=102eb726f63f3190, https://usegalaxy.org.au/published/workflow?id=106080375ad4eaaa, https://usegalaxy.org.au/published/workflow?id=218ffb4438833bdd, https://usegalaxy.org.au/published/workflow?id=57321b64220d5835, https://usegalaxy.org.au/published/workflow?id=8055596d732590d6, https://usegalaxy.org.au/published/workflow?id=8bc01c1fdd62ad12, https://usegalaxy.org/published/workflow?id=dd43ae9a5b303086, https://usegalaxy.org/published/workflow?id=ea3257e0ef9f505a, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/1256?version=1, https://workflowhub.eu/workflows/467?version=4, https://workflowhub.eu/workflows/468?version=3 single-cell/pseudobulk-analysis, single-cell/scatac-preprocessing-tenx, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_cell-cycle, single-cell/scrna-plant, single-cell/scrna-scanpy-pbmc3k
scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. 2019-07-18 http://bioconductor.org/packages/scater/ 1.22.0 bioconductor-scater 1.34.1 To update Single Cell, Transcriptomics, Visualization Read pre-processing, Sequencing quality control, Sequence visualisation Read pre-processing, Sequence visualisation RNA-Seq, Quality affairs, Molecular genetics RNA-Seq, Quality affairs, Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 349 365 1234 1397 0 0 0 0 29 29 1050 1050 0 0 0 0 378 1150 2284 7015 https://dev.workflowhub.eu/workflows/1241?version=2, https://usegalaxy.eu/published/workflow?id=f055b8fa294d4be8, https://usegalaxy.org.au/published/workflow?id=3c9140288202aa76 single-cell/scrna-scater-qc
sceasy_convert sceasy_convert Converter between difference single-cell formats 2023-11-10 https://github.com/cellgeni/sceasy/ 0.0.7 r-sceasy 0.0.7 Up-to-date Single Cell, Spatial Omics, Convert Formats Data handling Data handling iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy sceasy sceasy sceasy is a package that helps easy conversion of different single-cell data formats to each other. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 286 286 1379 1381 83 83 470 470 3 3 147 147 0 0 0 0 372 1116 1996 5990 https://dev.workflowhub.eu/workflows/1024?version=1, https://dev.workflowhub.eu/workflows/1025?version=1, https://dev.workflowhub.eu/workflows/1263?version=1, https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=9ed36a6849fa2014, https://usegalaxy.eu/published/workflow?id=a0f1959a9f4533f7, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d single-cell/EBI-retrieval, single-cell/scrna-case_alevin, single-cell/scrna-data-ingest
schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. 2019-12-16 https://github.com/joachimwolff/schicexplorer 4 schicexplorer 7 To update Sequence Analysis, Transcriptomics, Visualization, Single Cell Validation, Visualisation, Standardisation and normalisation Validation, Visualisation, Standardisation and normalisation Workflows, DNA, Chromosome conformation capture, ChIP-seq, Epigenetics Workflows, DNA, Chromosome conformation capture, ChIP-seq, Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer hicexplorer HiCExplorer A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.HiCExplorer — HiCExplorer 3.6 documentation.scHiCExplorer — scHiCExplorer 7 documentation.Free document hosting provided by Read the Docs. 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 77 78 793 813 10 10 23 23 16 16 685 685 0 0 0 0 103 310 1501 4523
scikit_bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics 2016-05-31 http://scikit-bio.org/ 0.4.2 scikit-bio 0.4.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 295 428 1488 2043 0 0 0 0 0 0 0 0 296 1021 1489 5022
scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. 2021-03-18 https://github.com/AdmiralenOla/Scoary 1.6.16 scoary 1.6.16 Up-to-date Metagenomics Analysis Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Genotype and phenotype, Model organisms, GWAS study, Functional genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 1120 1120 0 0 0 0 0 0 0 0 0 0 0 0 97 291 1120 3360
scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data 2018-08-12 http://bioconductor.org/packages/release/bioc/html/scPipe.html 1.0.0+galaxy2 bioconductor-scpipe 2.6.0 To update Transcriptomics, Single Cell Genome annotation, Validation, Alignment, Visualisation Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing Gene expression, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 38 254 632 61 61 786 786 1 1 1 1 0 0 0 0 94 288 1041 3501 https://usegalaxy.eu/published/workflow?id=0a692a2e643b9e1a
seaborn seaborn, seaborn_pairgrid Seaborn is a Python data visualization library based on Matplotlib. 2025-05-13 https://seaborn.pydata.org/ 0.13.2 seaborn To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seaborn https://github.com/galaxyproject/tools-iuc/tree/main/tools/seaborn 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
seacr seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. 2020-02-05 https://github.com/FredHutch/SEACR 1.3 seacr 1.3 Up-to-date Epigenetics, ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 131 131 5773 5773 267 267 7545 7545 0 0 0 0 0 0 0 0 398 1194 13318 39954 https://usegalaxy.eu/published/workflow?id=719314fa5263b501
selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. 2022-06-29 https://github.com/brsynth/selenzy-wrapper 0.3.0 selenzy_wrapper 0.3.0 Up-to-date Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks 2022-10-14 https://semibin.readthedocs.io/en/latest/ 2.0.2 semibin 2.2.0 To update Metagenomics Sequence assembly, Read binning Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Metagenomics, Machine learning, Microbial ecology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. 1 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 120 120 1862 1862 0 0 0 0 0 0 0 0 2 2 52 52 122 366 1914 5742 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=b0377f05f97b18b1
seq2hla seq2hla Precision HLA typing and expression from RNAseq data 2020-02-20 https://github.com/TRON-Bioinformatics/seq2HLA 2.3 seq2hla 2.3 Up-to-date Sequence Analysis Read mapping, Genetic variation analysis Read mapping, Genetic variation analysis Transcriptomics, Mapping Transcriptomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 51 51 382 382 1 1 6 6 2 2 45 45 0 0 0 0 54 162 433 1299 https://dev.workflowhub.eu/workflows/1381?version=1, https://usegalaxy.eu/published/workflow?id=c3f2350f0be2d9c9, https://usegalaxy.org.au/published/workflow?id=2249ab6710f5e84d, https://usegalaxy.org/published/workflow?id=1d925422fc6094a0 proteomics/neoantigen-6-predicting-hla-binding
seqcomplexity seqcomplexity Sequence complexity for raw reads 2022-06-07 https://github.com/stevenweaver/seqcomplexity 0.1.2 seqcomplexity 0.1.2 Up-to-date Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 76 76 51 51 126 126 0 0 0 0 0 0 0 0 72 216 202 606
seqkit seqkit_fx2tab, seqkit_head, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation 2022-06-01 https://bioinf.shenwei.me/seqkit/ 2.10.0 seqkit 2.10.0 Up-to-date Sequence Analysis DNA transcription, Sequence trimming, DNA translation, Sequence conversion DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis Database management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. 0 6 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 403 403 8889 8889 0 0 0 0 81 81 646 646 90 90 551 551 574 1722 10086 30258 https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56, https://workflowhub.eu/workflows/601?version=2, https://workflowhub.eu/workflows/602?version=2, https://workflowhub.eu/workflows/697?version=1
seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. 2024-01-15 https://github.com/jstjohn/SeqPrep 1.3.2 seqprep 1.3.2 Up-to-date Fastq Manipulation, Sequence Analysis Nucleic acid design Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Genomics, Sequence assembly, Sequencing, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 150 150 2742 2742 0 0 0 0 0 0 0 0 0 0 0 0 150 450 2742 8226
seqsero2 seqsero2 Salmonella serotype prediction from genome sequencing data 2023-11-07 https://github.com/denglab/SeqSero2 1.3.1 seqsero2 1.3.1 Up-to-date Sequence Analysis Genome indexing, Antimicrobial resistance prediction, Genome alignment Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Whole genome sequencing, Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 seqsero2 SeqSero2 rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode) 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 74 74 13134 13134 0 0 0 0 0 0 0 0 0 0 0 0 74 222 13134 39402 https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://workflowhub.eu/workflows/407?version=1
seqtk seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats 2015-01-13 https://github.com/lh3/seqtk 1.4 seqtk 1.5 To update Sequence Analysis Data handling, Sequence file editing Data handling, Sequence file editing Data management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 14 0 14 0 0 0 0 0 0 15 0 0 0 0 0 15 15 14 14 2479 2636 148593 150608 2541 3010 103334 112294 783 783 156492 156492 143 143 18259 18259 5946 18464 426678 1291009 https://dev.workflowhub.eu/workflows/1099?version=1, https://dev.workflowhub.eu/workflows/1116?version=1, https://dev.workflowhub.eu/workflows/1132?version=2, https://dev.workflowhub.eu/workflows/1197?version=2, https://dev.workflowhub.eu/workflows/1276?version=2, https://dev.workflowhub.eu/workflows/1287?version=2, https://dev.workflowhub.eu/workflows/1292?version=2, https://dev.workflowhub.eu/workflows/1307?version=1, https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=52cb9bacc26b013e, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=bc5ced57e711acf9, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=1a159863e9d977a0, https://usegalaxy.org.au/published/workflow?id=324c683a8e2fa5b0, https://usegalaxy.org.au/published/workflow?id=462beb964c99619d, https://usegalaxy.org.au/published/workflow?id=5cfea39918e8632d, https://usegalaxy.org.au/published/workflow?id=79ca45e45d76871f, https://usegalaxy.org.au/published/workflow?id=9c60b83feaa22415, https://usegalaxy.org.au/published/workflow?id=b59fada651043735, https://usegalaxy.org.au/published/workflow?id=fc3c83b11f527977, https://usegalaxy.org/published/workflow?id=1ddabc7d272dc702, https://usegalaxy.org/published/workflow?id=3269026bb1e0ec42, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=34f3aac3aed0f97a, https://usegalaxy.org/published/workflow?id=35c2626849348f2c, https://usegalaxy.org/published/workflow?id=51f936d1a4e849fa, https://usegalaxy.org/published/workflow?id=69514a75e4c9af08, https://usegalaxy.org/published/workflow?id=7610b7797d71993a, https://usegalaxy.org/published/workflow?id=cdea4f88ccbd155f, https://workflowhub.eu/workflows/1260?version=1, https://workflowhub.eu/workflows/517?version=1, https://workflowhub.eu/workflows/518?version=1, https://workflowhub.eu/workflows/880?version=1 assembly/assembly-with-preprocessing, assembly/metagenomics-assembly, contributing/create-new-tutorial, microbiome/metagenomics-assembly, sequence-analysis/Manage_AB1_Sanger, sequence-analysis/human-reads-removal, variant-analysis/aiv-analysis
sequali sequali Fast sequencing data quality metrics for short and long reads 2025-03-19 https://sequali.readthedocs.io/ 1.0.1 sequali 1.0.1 Up-to-date Fastq Manipulation Sequencing quality control, Statistical calculation Sequencing quality control, Statistical calculation Data quality management, Sequence analysis Data quality management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali https://github.com/galaxyproject/tools-iuc/tree/main/tools/sequali sequali Sequali Fast sequencing data quality metrics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
seqwish seqwish Alignment to variation graph inducer 2020-04-06 https://github.com/ekg/seqwish 0.7.5 seqwish 0.7.11 To update Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2 2 271 271 0 0 0 0 0 0 0 0 0 0 0 0 2 6 271 813 https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40
seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics 2018-08-20 https://satijalab.org/seurat/ 5.0 r-seurat 3.0.2 To update Single Cell, Transcriptomics, Sequence Analysis RNA-Seq, Transcriptomics RNA-Seq, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat seurat Seurat Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. 7 7 7 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 101 101 2188 2188 53 53 655 655 2 2 96 96 2 2 28 28 158 474 2967 8901 https://dev.workflowhub.eu/workflows/1375?version=1, https://dev.workflowhub.eu/workflows/1388?version=1, https://dev.workflowhub.eu/workflows/1389?version=1, https://usegalaxy.eu/published/workflow?id=10c5d0560b977a6f, https://usegalaxy.eu/published/workflow?id=26deb6f2521742ea, https://usegalaxy.eu/published/workflow?id=290373b2f5fb8c6c, https://usegalaxy.eu/published/workflow?id=c52e8b5ab3e8e958, https://usegalaxy.eu/published/workflow?id=d773cbc76253afbf single-cell/scrna-case_FilterPlotandExplore_SeuratTools, single-cell/scrna-seurat-pbmc3k
sfold sfold Predict the probable RNA secondary structures through structure ensemble sampling 2024-10-09 https://github.com/Ding-RNA-Lab/Sfold 2.2.0 To update RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold https://github.com/galaxyproject/tools-iuc/tree/main/tools/sfold 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
shasta shasta Fast de novo assembly of long read sequencing data 2020-11-11 https://github.com/chanzuckerberg/shasta 0.6.0 shasta 0.14.0 To update Assembly, Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 351 351 1166 1166 0 0 0 0 81 81 644 644 0 0 0 0 432 1296 1810 5430
shorah_amplicon shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode 2018-11-27 https://github.com/cbg-ethz/shorah/blob/master/README.md 1.1.3 shorah 1.99.2 To update Sequence Analysis Haplotype mapping, Variant calling Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics Metagenomics, Sequencing, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
shovill shovill Faster de novo assembly pipeline based around Spades 2017-10-24 https://github.com/tseemann/shovill 1.1.0 shovill 1.1.0 Up-to-date Assembly Genome assembly Genome assembly Genomics, Microbiology, Sequence assembly Genomics, Microbiology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2671 2807 52210 55759 4558 4565 48711 48739 1186 1354 22742 25911 68 68 4582 4582 8483 25760 128245 391481 https://dev.workflowhub.eu/workflows/1135?version=2, https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7, https://usegalaxy.eu/published/workflow?id=4216424f032c055f, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=b5ffba506152b1a1, https://usegalaxy.eu/published/workflow?id=b93333efdab316d8, https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5, https://usegalaxy.eu/published/workflow?id=fca458178b3c794a, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=52065a4100b11184, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f, https://usegalaxy.org.au/published/workflow?id=f2541030f6d70b59, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=0e30324072570abb, https://usegalaxy.org/published/workflow?id=4161cfd67ed94b5d, https://usegalaxy.org/published/workflow?id=4d1279007d0137fa, https://usegalaxy.org/published/workflow?id=9ac1e4efe310b3b3, https://usegalaxy.org/published/workflow?id=9e5c5ddb60a24889, https://usegalaxy.org/published/workflow?id=c454c930ccfb0d3f, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=db08887d7d6dc147, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/102?version=1, https://workflowhub.eu/workflows/103?version=1, https://workflowhub.eu/workflows/1043?version=7, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 assembly/mrsa-illumina
sickle sickle A windowed adaptive trimming tool for FASTQ files using quality 2015-11-03 https://github.com/najoshi/sickle 1.33.3 sickle-trim 1.33 To update Fastq Manipulation, Sequence Analysis Sequence trimming Sequence trimming Data quality management Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 565 645 18545 19406 1210 1213 11345 11349 0 0 0 0 103 104 948 1006 1878 5718 30838 93437 https://usegalaxy.eu/published/workflow?id=b6eb5fe7e37f680a, https://usegalaxy.fr/published/workflow?id=334189184455d9a2, https://usegalaxy.fr/published/workflow?id=74b4d11c07f7f0a4, https://usegalaxy.org/published/workflow?id=fca70e1bf761c6a2
simpleweather simple_weather provides simple weather in text format 2016-07-19 http://wttr.in/ 0.1.2 curl To update Visualization, Web Services iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. 2021-02-28 https://github.com/dlal-group/simtext 0.0.2 r-argparse 1.0.1 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tools/simtext https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 74 74 234 234 0 0 0 0 10 10 500 500 0 0 0 0 84 252 734 2202 https://dev.workflowhub.eu/workflows/1310?version=1 statistics/text-mining_simtext
sina sina SINA reference based multiple sequence alignment 2019-10-11 https://sina.readthedocs.io/en/latest/ 1.7.2 sina 1.7.2 Up-to-date Sequence Analysis Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 129 132 1388 1442 438 439 2449 2452 0 0 0 0 0 0 0 0 567 1705 3837 11568
sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools 2023-04-12 https://github.com/timoast/sinto 0.10.1 sinto 0.10.1 Up-to-date Single Cell, Epigenetics Bioinformatics, Cell biology Bioinformatics, Cell biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto sinto sinto Sinto is a toolkit for processing aligned single-cell data. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 81 81 332 332 49 49 211 211 2 2 90 90 0 0 0 0 132 396 633 1899 https://dev.workflowhub.eu/workflows/1012?version=1, https://dev.workflowhub.eu/workflows/1208?version=1 single-cell/scatac-preprocessing-tenx
slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads 2018-10-05 http://t-neumann.github.io/slamdunk 0.4.3 slamdunk 0.4.3 Up-to-date RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 12 16 241 362 75 75 1166 1166 0 0 0 0 0 0 0 0 87 265 1407 4342
sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. 2023-05-30 https://github.com/pachterlab/sleuth 0.30.2 r-sleuth 0.30.2 Up-to-date Transcriptomics, RNA, Statistics Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-Seq, Gene expression, Statistics and probability RNA-Seq, Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 34 34 181 181 0 0 0 0 0 0 0 0 0 0 0 0 34 102 181 543
smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. 2023-05-30 https://github.com/cbg-ethz/smallgenomeutilities 0.5.2 smallgenomeutilities 0.5.2 Up-to-date Sequence Analysis Read pre-processing, Sequence alignment, Genetic variation analysis Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Genomics, Population genetics, Workflows, Virology, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 159 159 0 0 0 0 0 0 0 0 0 0 0 0 9 27 159 477
smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing 2022-06-30 https://github.com/KamilSJaron/smudgeplot 0.2.5 smudgeplot 0.4.0 To update Assembly Sequence trimming, Genotyping, k-mer counting Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Sequence assembly, Genetic variation, Mathematics galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 95 95 516 516 68 68 180 180 69 69 1064 1064 0 0 0 0 232 696 1760 5280 https://dev.workflowhub.eu/workflows/1127?version=3, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/603?version=2, https://workflowhub.eu/workflows/698?version=1 assembly/ERGA-post-assembly-QC
snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. 2017-10-12 https://github.com/KorfLab/SNAP 2013_11_29 snap 2013_11_29 Up-to-date Sequence Analysis Gene prediction Gene prediction DNA, DNA polymorphism, Genetics DNA polymorphism, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 332 374 1482 1705 265 265 837 837 91 91 522 522 0 0 0 0 688 2106 2841 8746 https://dev.workflowhub.eu/workflows/1164?version=2, https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c genome-annotation/annotation-with-maker
snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis 2024-05-16 https://kzhang.org/SnapATAC2/ 2.6.4 To update Single Cell, Epigenetics Essential dynamics, Dimensionality reduction, Gene expression profiling Essential dynamics, Dimensionality reduction, Gene expression profiling Epigenomics, Cell biology, Chromosome conformation capture, Mapping, Sequencing Epigenomics, Cell biology, Chromosome conformation capture, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 snapatac SnapATAC SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq) is a fast, accurate and comprehensive method for analyzing single cell ATAC-seq datasets. 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 1983 1983 12 12 41 41 4 4 817 817 0 0 0 0 37 111 2841 8523 https://dev.workflowhub.eu/workflows/1343?version=2, https://usegalaxy.eu/published/workflow?id=15cb6b690d23e6ef, https://usegalaxy.eu/published/workflow?id=d20fbb95f15386f5, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/1078?version=1, https://workflowhub.eu/workflows/1089?version=1 single-cell/scatac-batch-correction-snapatac2, single-cell/scatac-standard-processing-snapatac2
sniffles sniffles Galaxy wrapper for sniffles 2020-08-29 https://github.com/fritzsedlazeck/Sniffles 2.5.2 sniffles 2.6.2 To update Sequence Analysis Sequence analysis, Structural variation detection Sequence analysis, Structural variation detection DNA structural variation, Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 165 165 1459 1459 199 199 1213 1213 93 93 2457 2457 4 4 11 11 461 1383 5140 15420 https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=35a9136ddf37d589, https://usegalaxy.eu/published/workflow?id=cb54883452a73019, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=d69a765cfc82a399
snipit snipit Summarise snps relative to a reference sequence 2022-07-17 https://github.com/aineniamh/snipit 1.6 snipit 1.6 Up-to-date Variant Analysis, Sequence Analysis Base position variability plotting Base position variability plotting Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit snipit snipit Summarise snps relative to a reference sequence 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 51 51 1039 1039 0 0 0 0 0 0 0 0 0 0 0 0 51 153 1039 3117 https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=bc5ced57e711acf9, https://workflowhub.eu/workflows/1260?version=1
snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps 2017-07-13 https://github.com/tseemann/snippy snippy 4.6.0 To update Sequence Analysis Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics Genomics, Model organisms, DNA polymorphism, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 3943 4255 133997 139604 4405 4462 112614 113142 2756 3283 54757 60816 46 46 1918 1918 11150 34346 303286 922052 https://dev.workflowhub.eu/workflows/1008?version=1, https://dev.workflowhub.eu/workflows/1069?version=2, https://dev.workflowhub.eu/workflows/1093?version=2, https://dev.workflowhub.eu/workflows/121?version=1, https://dev.workflowhub.eu/workflows/1305?version=2, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=464b642261ed7452, https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=65249196143d7930, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=920aab45ff028ed4, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a183da6b56cd1d60, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=1719e0eb54b41f68, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=5674956f5c18b85b, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://usegalaxy.org/published/workflow?id=ee4679b3e9e830b7, https://workflowhub.eu/workflows/1035?version=1 evolution/mtb_transmission, variant-analysis/microbial-variants, variant-analysis/tb-variant-analysis
snp_dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment 2019-10-18 https://github.com/tseemann/snp-dists 0.8.2 snp-dists 0.8.2 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 937 939 7877 7933 238 238 6107 6107 204 204 1353 1353 0 0 0 0 1379 4139 15337 46067 https://dev.workflowhub.eu/workflows/1009?version=1, https://dev.workflowhub.eu/workflows/1309?version=2, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6d333ed886aab471, https://usegalaxy.eu/published/workflow?id=8a248dda0131e8ad, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=d5cf994c03a60fa4, https://usegalaxy.eu/published/workflow?id=e97b938ca4723827, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55 evolution/mtb_transmission
snp_sites snp_sites Finds SNP sites from a multi-FASTA alignment file 2017-06-28 https://github.com/sanger-pathogens/snp-sites 2.5.1 snp-sites 2.5.1 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 766 770 7626 7710 333 333 1981 1981 134 134 1794 1794 0 0 0 0 1233 3703 11401 34287 https://dev.workflowhub.eu/workflows/1009?version=1, https://dev.workflowhub.eu/workflows/1309?version=2, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=6d333ed886aab471, https://usegalaxy.eu/published/workflow?id=8a248dda0131e8ad evolution/mtb_transmission
snpeff snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox 2014-11-11 http://snpeff.sourceforge.net/ 5.2 biopython 1.70 To update Genome-Wide Association Study, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff 5 5 5 5 0 0 0 0 0 0 0 1 0 0 0 0 5 5 0 0 0 0 0 0 5 0 0 0 0 0 5 5 5 0 8061 8982 117010 122981 16913 24795 121063 191088 2266 2515 13252 14899 694 694 3881 3902 27934 92854 255206 843282 https://dev.workflowhub.eu/workflows/1063?version=1, https://dev.workflowhub.eu/workflows/1081?version=1, https://dev.workflowhub.eu/workflows/1096?version=2, https://dev.workflowhub.eu/workflows/1104?version=1, https://dev.workflowhub.eu/workflows/1108?version=1, https://dev.workflowhub.eu/workflows/1114?version=1, https://dev.workflowhub.eu/workflows/41?version=1, 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introduction/galaxy-intro-ngs-data-managment, variant-analysis/dip, variant-analysis/exome-seq, variant-analysis/mapping-by-sequencing, variant-analysis/somatic-variants, variant-analysis/trio-analysis
snpeff_sars_cov_2 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox 2020-06-17 http://snpeff.sourceforge.net/ To update Genome-Wide Association Study, Variant Analysis SNP detection SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs DNA polymorphism, Nucleic acid sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 snpeff snpEff Variant annotation and effect prediction tool. 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snpfreqplot snpfreqplot A plotting app to visualise the SNPs across a region 2020-12-02 https://github.com/BrownfieldPlantLab/SNPFreqPlot 1.0 r-base To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 364 364 3756 3756 474 474 1514 1514 97 97 1187 1187 9 9 321 321 944 2832 6778 20334 https://dev.workflowhub.eu/workflows/199?version=2, https://usegalaxy.eu/published/workflow?id=036990ecf300a99f, https://usegalaxy.eu/published/workflow?id=05bd1d9c61df5d16, https://usegalaxy.eu/published/workflow?id=0c94260298199d8b, https://usegalaxy.eu/published/workflow?id=20592f292c205954, https://usegalaxy.eu/published/workflow?id=27fca972f1d1a312, https://usegalaxy.eu/published/workflow?id=2d509fad86eb97fb, https://usegalaxy.eu/published/workflow?id=37b04b02ec08e84f, https://usegalaxy.eu/published/workflow?id=70ec8b1719e25982, https://usegalaxy.eu/published/workflow?id=88f5cef7e4146520, https://usegalaxy.eu/published/workflow?id=9eb29cc96d8d75c2, https://usegalaxy.eu/published/workflow?id=eb03839cc36048f5, https://usegalaxy.fr/published/workflow?id=798c8ff19825ab2c, https://usegalaxy.fr/published/workflow?id=b168a179d1b456cb, https://usegalaxy.org.au/published/workflow?id=1764bb1f506212e8, https://usegalaxy.org.au/published/workflow?id=1782d699b0166725, https://usegalaxy.org.au/published/workflow?id=5a975438c8752269, https://usegalaxy.org.au/published/workflow?id=7a0b3968968c5994, https://usegalaxy.org.au/published/workflow?id=7cc2b5010c56f117, https://usegalaxy.org.au/published/workflow?id=800d28ec61b15244, https://usegalaxy.org.au/published/workflow?id=8e2b94c6fbf44368, https://usegalaxy.org.au/published/workflow?id=989eb73372135796, https://usegalaxy.org.au/published/workflow?id=b601f48ecec15bf4, https://usegalaxy.org.au/published/workflow?id=b920b02a23f94d11, https://usegalaxy.org.au/published/workflow?id=d0d6743450e5060d, https://usegalaxy.org.au/published/workflow?id=fbc732db2a2821b0, https://usegalaxy.org/published/workflow?id=07e761b2501971c6, https://usegalaxy.org/published/workflow?id=2967ef82911f2cca, https://usegalaxy.org/published/workflow?id=2b09f3c9465ee054, https://usegalaxy.org/published/workflow?id=2dceaa255cc8cf83, https://usegalaxy.org/published/workflow?id=6c2bb2209aad5e44, https://usegalaxy.org/published/workflow?id=7af656b8ea5e7e2e, https://usegalaxy.org/published/workflow?id=8a01c78688beae1d, https://usegalaxy.org/published/workflow?id=dcbc71347300822d, https://usegalaxy.org/published/workflow?id=f58c90061c31bd48, https://usegalaxy.org/published/workflow?id=ff3ade25b35f4893, https://workflowhub.eu/workflows/109?version=9
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https://usegalaxy.org/published/workflow?id=ffae9c47980a5170, https://workflowhub.eu/workflows/1063?version=3, https://workflowhub.eu/workflows/109?version=9, https://workflowhub.eu/workflows/110?version=10, https://workflowhub.eu/workflows/1190?version=1, https://workflowhub.eu/workflows/138?version=5, https://workflowhub.eu/workflows/354?version=1, https://workflowhub.eu/workflows/356?version=1, https://workflowhub.eu/workflows/35?version=1, https://workflowhub.eu/workflows/36?version=1, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1 galaxy-interface/collections, galaxy-interface/workflow-automation, introduction/galaxy-intro-ngs-data-managment, microbiome/pathogen-detection-from-nanopore-foodborne-data, variant-analysis/sars-cov-2
snpsift_dbnsfp snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP snpsift 5.2 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 24 52 55 75 75 423 423 0 0 0 0 0 0 0 0 98 295 475 1428
snpsift_genesets snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html#geneSets snpsift 5.2 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 105 135 514 569 201 202 496 499 0 0 0 0 0 0 0 0 306 949 1010 3088
socru socru Order and orientation of complete bacterial genomes 2019-09-03 https://github.com/quadram-institute-bioscience/socru 2.1.7 socru 2.2.4 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 40 45 591 665 98 98 309 309 0 0 0 0 0 0 0 0 138 419 900 2774
sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. 2021-09-16 https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 Up-to-date Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 3
spacexr spacexr_cside, spacexr_rctd Cell type identification and cell type-specific differential expression in spatial transcriptomics 2024-08-02 https://github.com/dmcable/spacexr/tree/master 2.2.1 r-spacexr 2.2.1 Up-to-date Spatial Omics, Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr https://github.com/galaxyproject/tools-iuc/tree/main/tools/spacexr 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. 2016-12-21 https://github.com/ablab/spades 4.2.0 spades 4.2.0 Up-to-date Assembly, RNA, Metagenomics Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades spades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. 9 9 9 9 0 0 0 0 0 0 0 0 0 0 0 1 3 8 0 0 0 0 0 0 3 0 0 0 0 0 3 9 3 0 9662 10144 91363 98738 17182 17206 135480 135565 6123 7206 58637 67930 401 402 2137 2184 33368 101694 287617 879651 https://dev.workflowhub.eu/workflows/1103?version=1, https://dev.workflowhub.eu/workflows/1120?version=1, https://dev.workflowhub.eu/workflows/1124?version=1, https://dev.workflowhub.eu/workflows/39?version=1, https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09, https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://usegalaxy.eu/published/workflow?id=7b755497d168cb13, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=a847773b563b2328, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=c702c76cadebac30, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=db10c092fad70d69, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.fr/published/workflow?id=5bb882218afda132, https://usegalaxy.org.au/published/workflow?id=38d992baf9a2a2bc, https://usegalaxy.org.au/published/workflow?id=39c724282ee008e3, https://usegalaxy.org.au/published/workflow?id=813a4938397cf6ee, https://usegalaxy.org.au/published/workflow?id=87cdeb05b1ebeab0, https://usegalaxy.org.au/published/workflow?id=8abcfe166f1a6cd8, https://usegalaxy.org.au/published/workflow?id=8f7d5ebead46a6d0, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=15cca0e249f40aea, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=5039ae2c81d0aba8, https://usegalaxy.org/published/workflow?id=71f8a4090877f171, https://usegalaxy.org/published/workflow?id=8a350e0d96e937a5, https://usegalaxy.org/published/workflow?id=ae81cc0e8263d03e, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://workflowhub.eu/workflows/434?version=1, https://workflowhub.eu/workflows/52?version=1, https://workflowhub.eu/workflows/68?version=1 assembly/debruijn-graph-assembly, assembly/metagenomics-assembly, microbiome/metagenomics-assembly
spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. 2019-01-11 http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ 2.4.9 python To update Sequence Analysis, Genome annotation iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 89 103 416 511 309 309 4400 4400 0 0 0 0 0 0 0 0 398 1208 4816 14543
spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. 2024-08-25 https://github.com/theislab/spapros 0.1.5 spapros 0.1.5 Up-to-date Single Cell, Transcriptomics, Sequence Analysis Primer and probe design, Visualisation Primer and probe design, Visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros spapros spapros Spapros is a python package that provides a pipeline for probe set selection and evaluation for targeted spatial transcriptomics data. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 3 3 0 0 0 0 0 0 0 0 0 0 0 0 1 3 3 9
spotyping spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads 2018-05-07 https://github.com/xiaeryu/SpoTyping-v2.0 2.1 spotyping 2.1 Up-to-date Sequence Analysis Variant pattern analysis Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 30 30 1884 1884 0 0 0 0 0 0 0 0 0 0 0 0 30 90 1884 5652
spyboat spyboat Wavelet analysis for 3d-image stacks 2020-11-28 http://github.com/tensionhead/spyboat 0.1.2 spyboat To update Imaging, Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 5 5 154 154 0 0 0 0 0 0 0 0 0 0 0 0 5 15 154 462
squirrel squirrel_phylo, squirrel_qc QC and Phylogenetic analysis of MPXV 2025-01-16 https://github.com/aineniamh/squirrel 1.0.13 squirrel 1.1.3 To update Phylogenetics Phylogenetic analysis, Sequencing quality control Phylogenetic analysis, Sequencing quality control Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel squirrel squirrel Some QUIck Reconstruction to Resolve Evolutionary LinksSquirrel provides a rapid way of producing reliable alignments for MPXV and also enable maximum-likelihood phylogenetics pipeline tree estimation. 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens 2022-08-22 http://katholt.github.io/srst2/ 0.2.0 samtools 1.22 To update Metagenomics Multilocus sequence typing Multilocus sequence typing Whole genome sequencing, Public health and epidemiology, Comparative genomics Whole genome sequencing, Public health and epidemiology, Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 42 42 316 316 1 1 71 71 0 0 0 0 0 0 0 0 43 129 387 1161 https://workflowhub.eu/workflows/407?version=1
stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq 2016-03-07 http://catchenlab.life.illinois.edu/stacks/ stacks 2.68 To update Sequence Analysis Data handling Data handling Mapping, Population genetics Mapping, Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. 0 13 13 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 13 13 0 497 639 6889 12825 0 0 0 0 158 158 5253 5253 3 3 8 8 658 2116 12150 42386 https://dev.workflowhub.eu/workflows/1216?version=1, https://dev.workflowhub.eu/workflows/1245?version=2, https://dev.workflowhub.eu/workflows/1250?version=2, https://dev.workflowhub.eu/workflows/1286?version=2 ecology/de-novo-rad-seq, ecology/genetic-map-rad-seq, ecology/ref-based-rad-seq
stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq 2018-12-01 http://catchenlab.life.illinois.edu/stacks/ 2.55 stacks 2.68 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 696 734 8504 9239 0 0 0 0 321 321 19419 19419 29 29 609 609 1046 3176 28532 86331 https://usegalaxy.eu/published/workflow?id=510bcef37f385495, https://usegalaxy.eu/published/workflow?id=f5d387583670f694, https://usegalaxy.org.au/published/workflow?id=1e71b5232b9b4d2a, https://usegalaxy.org.au/published/workflow?id=9b3f3d331d0b2892, https://usegalaxy.org.au/published/workflow?id=a401ad5349b44dfb, https://usegalaxy.org.au/published/workflow?id=ca45322bff44e73a, https://usegalaxy.org.au/published/workflow?id=f7adc76331620f34, https://workflowhub.eu/workflows/347?version=1, https://workflowhub.eu/workflows/348?version=1, https://workflowhub.eu/workflows/349?version=1, https://workflowhub.eu/workflows/350?version=1, https://workflowhub.eu/workflows/352?version=1
star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR 2015-10-15 https://github.com/STAR-Fusion/STAR-Fusion 0.5.4-3+galaxy1 star-fusion 1.15.0 To update Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 102 1299 1411 215 316 2050 3171 4 4 231 231 0 0 0 0 304 1030 3580 11973
staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. 2024-09-19 https://github.com/phac-nml/staramr 0.11.0 staramr 0.11.0 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/staramr https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr staramr staramr staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2391 2435 25572 26123 1703 1703 11898 11898 952 952 7888 7888 52 52 5414 5414 5098 15338 50772 152867 https://dev.workflowhub.eu/workflows/1107?version=1, https://dev.workflowhub.eu/workflows/1168?version=2, https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=201e65bcf2b71584, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=7, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/470?version=1 genome-annotation/amr-gene-detection, microbiome/plasmid-metagenomics-nanopore
straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model 2022-10-02 https://github.com/brsynth/straindesign 3.2.2 straindesign 3.2.3 To update Systems Biology, Synthetic Biology iuc https://github.com/brsynth/straindesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
strelka strelka_germline, strelka_somatic Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. 2021-01-27 https://github.com/Illumina/strelka/ 2.9.10 strelka 2.9.10 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 138 138 882 882 550 550 1711 1711 0 0 0 0 0 0 0 0 688 2064 2593 7779 https://usegalaxy.eu/published/workflow?id=ddd604341afd9cf7
stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. 2014-09-13 http://ccb.jhu.edu/software/stringtie/ 2.2.3 stringtie 3.0.0 To update Transcriptomics Transcriptome assembly, RNA-Seq analysis Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-Seq Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. 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proteomics/neoantigen-2-non-reference-database-generation, proteomics/proteogenomics-dbcreation, transcriptomics/de-novo, transcriptomics/differential-isoform-expression
structure structure for using multi-locus genotype data to investigate population structure. 2017-09-22 https://web.stanford.edu/group/pritchardlab/structure.html 2.3.4 structure 2.3.4 Up-to-date Phylogenetics, Variant Analysis Genetic variation analysis Genetic variation analysis Population genetics Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 125 134 3289 3484 0 0 0 0 0 0 0 0 3 3 330 330 128 393 3619 11052
structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method 2017-12-06 http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ 0.6.94 structureharvester 0.6.94 Up-to-date Phylogenetics, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. 2021-04-05 https://github.com/wtsi-hpag/PretextSnapshot 0.0.7 pretextgraph 0.0.9 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 3 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 610 610 3973 3973 303 303 3305 3305 75 75 1375 1375 0 0 0 0 988 2964 8653 25959 https://dev.workflowhub.eu/workflows/1002?version=1, https://dev.workflowhub.eu/workflows/1127?version=3, https://dev.workflowhub.eu/workflows/1187?version=2, https://usegalaxy.eu/published/workflow?id=069d99391a69baf4, https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920, https://usegalaxy.eu/published/workflow?id=3010ecad1a342331, https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f, https://usegalaxy.eu/published/workflow?id=3b57fc81001667b5, https://usegalaxy.eu/published/workflow?id=4949751217c0e211, https://usegalaxy.eu/published/workflow?id=652433160b04b232, https://usegalaxy.eu/published/workflow?id=792b24fc23bd3071, https://usegalaxy.eu/published/workflow?id=a37d1e0db16cfb67, https://usegalaxy.eu/published/workflow?id=a53f78aa6866b811, https://usegalaxy.eu/published/workflow?id=b287bb779cf686ef, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=bc8ccd13a07bd9ec, https://usegalaxy.eu/published/workflow?id=c8f94a2e838fc0f1, https://usegalaxy.eu/published/workflow?id=feeb1fa358ccf328, https://usegalaxy.org.au/published/workflow?id=0aa316f8c6cff444, https://usegalaxy.org.au/published/workflow?id=0dbb85f727302a72, https://usegalaxy.org.au/published/workflow?id=29f0c07c8a24b542, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=455e68f185fec41b, https://usegalaxy.org.au/published/workflow?id=6c1c11a81a2ab1b8, https://usegalaxy.org.au/published/workflow?id=6ec5728eec9c26d7, https://usegalaxy.org.au/published/workflow?id=7028436ef03171cc, https://usegalaxy.org.au/published/workflow?id=77b2fcf8c805ad5d, https://usegalaxy.org.au/published/workflow?id=7a97e8ccc332c1e8, https://usegalaxy.org.au/published/workflow?id=86eb0ea9dc230f04, https://usegalaxy.org.au/published/workflow?id=ae6a03240680712a, https://usegalaxy.org.au/published/workflow?id=b9e89401313a0cca, https://usegalaxy.org.au/published/workflow?id=be35847680078c90, https://usegalaxy.org.au/published/workflow?id=cac0b8a09d59044b, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467, https://usegalaxy.org.au/published/workflow?id=fdec6e2fcd5e2cf5, https://usegalaxy.org/published/workflow?id=155839aeb6340f54, https://usegalaxy.org/published/workflow?id=28dbbfb3d480f4b1, https://usegalaxy.org/published/workflow?id=28ddea356ae57da1, https://usegalaxy.org/published/workflow?id=3d805d7e0f34c727, https://usegalaxy.org/published/workflow?id=3db51822f04f4ff7, https://usegalaxy.org/published/workflow?id=6341c384ceaf47ed, https://usegalaxy.org/published/workflow?id=88327cb2e0fe3c25, https://usegalaxy.org/published/workflow?id=903e35b62946ed76, https://usegalaxy.org/published/workflow?id=9f4c4038d1c519e2, https://usegalaxy.org/published/workflow?id=a4a6d6846c1692f9, https://usegalaxy.org/published/workflow?id=afa89bb0e8966753, https://workflowhub.eu/workflows/1054?version=1, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/625?version=13, https://workflowhub.eu/workflows/702?version=1 assembly/ERGA-post-assembly-QC, assembly/vgp_genome_assembly
swiftlink swiftlink Parallel MCMC Linkage Analysis 2017-11-21 https://github.com/ajm/swiftlink 1.0 swiftlink 1.0 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
syndiva syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. 2022-06-23 1.0 clustalo 1.2.4 To update Proteomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 30 30 0 0 0 0 0 0 0 0 0 0 0 0 2 6 30 90
syri syri Synteny and Rearrangement Identifier 2025-04-16 https://github.com/schneebergerlab/syri 1.7.1 syri 1.7.1 Up-to-date Sequence Analysis Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping DNA polymorphism, Sequence assembly, DNA structural variation, Mapping, Sequencing DNA polymorphism, Sequence assembly, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri SyRI SyRI SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies.Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 7 7 1 3 7 21 https://usegalaxy.fr/published/workflow?id=356dced9687596b7, https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef
table_compute table_compute Perform general-purpose table operations 2019-06-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute 1.2.4 pandas To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1835 1950 225030 226201 1673 1679 13059 13124 262 262 16967 16967 69 69 735 735 3839 11638 255791 768609 https://dev.workflowhub.eu/workflows/1014?version=1, https://dev.workflowhub.eu/workflows/1083?version=1, https://dev.workflowhub.eu/workflows/1246?version=2, https://dev.workflowhub.eu/workflows/1326?version=3, https://dev.workflowhub.eu/workflows/1382?version=1, https://dev.workflowhub.eu/workflows/1392?version=1, https://usegalaxy.eu/published/workflow?id=020f877513f2d0d1, https://usegalaxy.eu/published/workflow?id=079e2a968d8e6176, 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tabular_to_fastq tabular_to_fastq Tabular to FASTQ converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 480 528 9526 11269 689 2285 10525 31353 84 113 862 1151 11 11 21 21 1264 5465 20934 85662 https://usegalaxy.eu/published/workflow?id=5e1b048040ea7535, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=acb9131e84de1ae0, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=1e1a299825f27f11, https://usegalaxy.org/published/workflow?id=1efb485f123233eb, https://usegalaxy.org/published/workflow?id=41b181f1d763e419, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=5de035c08af915ea, https://usegalaxy.org/published/workflow?id=86838846a266181d, https://usegalaxy.org/published/workflow?id=9304cc9410a96323, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9 single-cell/scrna-data-ingest
tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. 2016-05-05 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup 1.0.2 openjdk To update Statistics, SAM, Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13 16 112 164 40 75 703 870 0 0 0 0 0 0 0 0 53 197 815 2664
tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches 2020-04-19 https://github.com/nebiolabs/tasmanian-mismatch 1.0.7 tasmanian-mismatch 1.0.7 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 13 13 31 31 263 263 0 0 0 0 0 0 0 0 39 117 276 828 https://usegalaxy.org/published/workflow?id=1ddabc7d272dc702, https://usegalaxy.org/published/workflow?id=cdea4f88ccbd155f
taxonkit name2taxid, profile2cami TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit 2024-07-26 https://bioinf.shenwei.me/taxonkit/ 0.20.0 taxonkit 0.20.0 Up-to-date Metagenomics Formatting, Data retrieval Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Taxonomy, Biotechnology, Ecology iuc https://github.com/shenwei356/taxonkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 410 410 0 0 0 0 0 0 0 0 0 0 0 0 5 15 410 1230 https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1
taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy 2019-01-13 https://github.com/pvanheus/ncbitaxonomy 0.3.0 rust-ncbitaxonomy 1.0.7 To update Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile 2015-08-06 http://sourceforge.net/projects/krona/ 2.7.1+galaxy0 krona 2.8.1 To update Assembly Visualisation Visualisation Metagenomics Metagenomics crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 5929 6170 40535 41852 5636 6644 28814 35461 1722 1722 9176 9176 110 110 362 362 13397 41440 78887 244625 https://dev.workflowhub.eu/workflows/1064?version=1, https://dev.workflowhub.eu/workflows/1067?version=1, https://dev.workflowhub.eu/workflows/1073?version=1, https://dev.workflowhub.eu/workflows/1088?version=1, https://dev.workflowhub.eu/workflows/1095?version=1, 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microbiome/mothur-miseq-sop, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling
taxpasta taxpasta standardise taxonomic profiles 2023-08-30 https://taxpasta.readthedocs.io/en/latest/ 0.7.0 taxpasta 0.7.0 Up-to-date Sequence Analysis Standardisation and normalisation, Aggregation, Formatting, Conversion Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/taxprofiler/taxpasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 72 72 0 0 0 0 0 0 0 0 1 1 18 18 18 54 90 270 https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7
tb_variant_filter tb_variant_filter M. tuberculosis H37Rv VCF filter 2019-10-03 https://github.com/COMBAT-TB/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 Up-to-date Variant Analysis iuc https://github.com/COMBAT-TB/tb_variant_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 518 546 33883 34183 312 312 21754 21754 89 89 6762 6762 1 1 3000 3000 920 2788 65399 196497 https://dev.workflowhub.eu/workflows/1008?version=1, https://dev.workflowhub.eu/workflows/1009?version=1, https://dev.workflowhub.eu/workflows/1069?version=2, https://dev.workflowhub.eu/workflows/1305?version=2, https://dev.workflowhub.eu/workflows/1309?version=2, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=65249196143d7930, https://usegalaxy.eu/published/workflow?id=6d333ed886aab471, https://usegalaxy.eu/published/workflow?id=8a248dda0131e8ad, https://usegalaxy.eu/published/workflow?id=a183da6b56cd1d60, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1 evolution/mtb_transmission, variant-analysis/tb-variant-analysis
tbl2gff3 tbl2gff3 Table to GFF3 2020-07-07 https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 1.2 bcbiogff 0.6.6 To update Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 603 603 2276 2276 96 96 296 296 138 138 576 576 12 12 47 47 849 2547 3195 9585 https://dev.workflowhub.eu/workflows/1136?version=2, https://dev.workflowhub.eu/workflows/1168?version=2, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org/published/workflow?id=547f86db467bf620 genome-annotation/amr-gene-detection, genome-annotation/bacterial-genome-annotation
tbprofiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. 2019-04-02 https://github.com/jodyphelan/TBProfiler 6.4.0 delly 1.3.3 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 386 416 10098 10173 431 431 9375 9375 170 170 8119 8119 0 0 0 0 987 2991 27592 82851 https://dev.workflowhub.eu/workflows/1010?version=1, https://dev.workflowhub.eu/workflows/1069?version=2, https://dev.workflowhub.eu/workflows/1314?version=2, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=89ed570bc0703472, https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1 evolution/mtb_transmission, variant-analysis/tb-variant-analysis
tbvcfreport tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) 2019-08-29 https://github.com/COMBAT-TB/tbvcfreport 1.0.1 tbvcfreport 1.0.1 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 335 353 5946 5996 383 383 7199 7199 84 84 3177 3177 0 0 0 0 802 2424 16322 49016 https://dev.workflowhub.eu/workflows/1069?version=2, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1 variant-analysis/tb-variant-analysis
te_finder te_finder Transposable element insertions finder 2022-08-08 https://github.com/VistaSohrab/TEfinder 1.0.1 samtools 1.22 To update Sequence Analysis Genome indexing, Variant calling, PCR primer design Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 23 23 209 209 0 0 0 0 0 0 0 0 0 0 0 0 23 69 209 627
telescope_assign telescope_assign Single locus resolution of Transposable ELEment expression. 2019-09-03 https://github.com/mlbendall/telescope/ 1.0.3 telescope 1.0.3 Up-to-date Genome annotation Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. 2020-04-10 http://hammelllab.labsites.cshl.edu/software/ 2.2.3 tetranscripts 2.2.3 Up-to-date Sequence Analysis iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 85 1119 1119 0 0 0 0 4 4 127 127 0 0 0 0 89 267 1246 3738
tetyper tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. 2019-11-23 https://github.com/aesheppard/TETyper 1.1 tetyper 1.1 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 21 21 107 113 49 49 163 163 0 0 0 0 0 0 0 0 70 210 270 816
tn93 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences 2018-06-06 https://github.com/veg/tn93/ 1.0.14 tn93 1.0.14 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 46 46 1920 1920 231 231 2610 2610 0 0 0 0 0 0 0 0 277 831 4530 13590
tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files 2024-04-30 https://gitlab.com/ifb-elixirfr/abromics/tooldistillator 0.9.3 tooldistillator 0.9.3 Up-to-date Sequence Analysis Data parsing Microbiology, Bioinformatics, Sequence analysis Microbiology, Bioinformatics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 85 779 779 137 137 617 617 0 0 0 0 11 11 6503 6503 233 699 7899 23697 https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502, https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88, https://usegalaxy.eu/published/workflow?id=0c47571d20535426, https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=4216424f032c055f, https://usegalaxy.eu/published/workflow?id=47e14222073e7192, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91, https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=884a4415b669690c, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=b93333efdab316d8, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=ebb131f2a6172081, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.eu/published/workflow?id=fca458178b3c794a, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=0e30324072570abb, https://usegalaxy.org/published/workflow?id=1be5c982c2d36a6c, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=4161cfd67ed94b5d, https://usegalaxy.org/published/workflow?id=4d1279007d0137fa, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=623fc80c7f91a33a, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=9ac1e4efe310b3b3, https://usegalaxy.org/published/workflow?id=9e5c5ddb60a24889, https://usegalaxy.org/published/workflow?id=9f68718f025bed30, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=b6a795834009ce06, https://usegalaxy.org/published/workflow?id=c454c930ccfb0d3f, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1043?version=7, https://workflowhub.eu/workflows/1049?version=7, https://workflowhub.eu/workflows/1050?version=9, https://workflowhub.eu/workflows/1052?version=8
tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. 2024-03-28 https://github.com/cbib/TraceGroomer 0.1.4 tracegroomer 0.1.4 Up-to-date Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 11 11 0 0 0 0 0 0 0 0 4 4 41 41 5 15 52 156 https://usegalaxy.fr/published/workflow?id=879408d684923861
tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose A suite tools for basecalling, alignment, assembly and deconvolution of Sanger chromatograms using tracy. 2021-10-12 https://github.com/gear-genomics/tracy/ 0.7.8 tracy 0.7.8 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 139 139 3649 3649 0 0 0 0 0 0 0 0 0 0 0 0 139 417 3649 10947
transdecoder transdecoder TransDecoder finds coding regions within transcripts 2015-11-09 https://transdecoder.github.io/ 5.5.0 transdecoder 5.7.1 To update Transcriptomics, RNA Coding region prediction, de Novo sequencing, De-novo assembly Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1040 1093 6751 7408 1166 1166 6047 6047 359 391 2953 3250 35 35 465 467 2600 7885 16216 49604 https://dev.workflowhub.eu/workflows/1306?version=2, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.org.au/published/workflow?id=c04a62f528a69e79, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1, https://workflowhub.eu/workflows/879?version=1 transcriptomics/full-de-novo
transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT 2019-03-01 https://github.com/mad-lab/transit/ 3.2.3 transit 3.3.19 To update Genome annotation Transposon prediction Transposon prediction DNA, Sequencing, Mobile genetic elements DNA, Sequencing, Mobile genetic elements iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 187 195 1118 1157 489 523 2634 3717 60 60 501 501 0 0 0 0 736 2250 4253 13881 https://dev.workflowhub.eu/workflows/1149?version=2 genome-annotation/tnseq
transtermhp transtermhp Finds rho-independent transcription terminators in bacterial genomes 2015-10-08 https://transterm.cbcb.umd.edu transtermhp 2.09 To update Sequence Analysis Transcriptional regulatory element prediction Transcriptional regulatory element prediction Transcription factors and regulatory sites Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 55 450 462 50 50 190 190 0 0 0 0 0 0 0 0 105 315 640 1932
trimal trimal Tool for automated alignment trimming 2024-10-02 https://trimal.readthedocs.io 1.5.0 trimal 1.5.0 Up-to-date Sequence Analysis, Phylogenetics Multiple sequence alignment Multiple sequence alignment Sequence analysis, Sequencing, Sequence sites, features and motifs Sequence analysis, Sequencing, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal trimal trimAl Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 19 19 118 118 0 0 0 0 0 0 0 0 105 105 954 954 124 372 1072 3216 https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://usegalaxy.fr/published/workflow?id=e134e9637adfc5b6 sequence-analysis/tapscan-streptophyte-algae
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https://usegalaxy.org/published/workflow?id=f9d546aae406cf15, https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://usegalaxy.org/published/workflow?id=fc09d17e0bce18f8, https://usegalaxy.org/published/workflow?id=fd30cdfe7e38b508, https://usegalaxy.org/published/workflow?id=fe2c0e4694c56b6b, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86, https://workflowhub.eu/workflows/1271?version=1, https://workflowhub.eu/workflows/1272?version=1, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1, https://workflowhub.eu/workflows/628?version=1, https://workflowhub.eu/workflows/676?version=1, https://workflowhub.eu/workflows/876?version=1 epigenetics/tal1-binding-site-identification, evolution/mtb_transmission, sequence-analysis/human-reads-removal, transcriptomics/de-novo, transcriptomics/full-de-novo, variant-analysis/exome-seq, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants
trimns trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline 2021-01-29 https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs 0.1.0 trimns_vgp 1.0 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 48 48 0 0 0 0 0 0 0 0 0 0 0 0 24 72 48 144
trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq 2015-11-09 https://github.com/trinityrnaseq/trinityrnaseq 2.15.1 trinity 2.15.2 To update Transcriptomics, RNA Transcriptome assembly Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Transcriptomics, Gene transcripts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. 9 13 13 13 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 11 0 1 0 0 0 11 13 12 0 4727 5119 38023 43670 7433 7433 49692 49692 2166 2358 20372 26526 312 317 2957 3039 14638 44503 111044 345015 https://dev.workflowhub.eu/workflows/1306?version=2 transcriptomics/full-de-novo
trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. 2016-11-15 https://trinotate.github.io/ 3.2.2 trinotate 4.0.2 To update Transcriptomics, RNA Gene functional annotation Gene functional annotation Gene expression, Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 397 423 2068 2239 556 556 2051 2051 170 209 938 1178 0 1 0 10 1123 3435 5057 15592 https://dev.workflowhub.eu/workflows/1306?version=2 transcriptomics/full-de-novo
trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers 2021-02-11 https://github.com/rrwick/Trycycler 0.5.5 trycycler 0.5.5 Up-to-date Assembly Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler trycycler Trycycler Trycycler: consensus long-read assemblies for bacterial genomes 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 292 292 14972 14972 0 0 0 0 160 160 5076 5076 10 10 27 27 462 1386 20075 60225
tsebra tsebra This tool has been developed to combine BRAKER predictions. 2023-10-19 https://github.com/Gaius-Augustus/TSEBRA 1.1.2.5 tsebra 1.1.2.5 Up-to-date Genome annotation Homology-based gene prediction, Alternative splicing prediction Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Gene expression, RNA-Seq, Gene transcripts, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 43 43 0 0 0 0 0 0 0 0 0 0 0 0 13 39 43 129
tsne tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation 2017-05-26 https://cran.r-project.org/web/packages/Rtsne/ 0.0.2 r-rtsne 0.13 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 29 38 222 381 65 65 299 299 0 0 0 0 2 2 4 4 96 297 525 1734
tximport tximport Wrapper for the Bioconductor package tximport 2019-10-15 http://bioconductor.org/packages/tximport/ 1.30.0 bioconductor-tximport 1.34.0 To update Transcriptomics Pathway or network analysis, Formatting, RNA-Seq analysis Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Transcriptomics, Gene transcripts, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 247 249 2040 2061 954 954 7413 7413 0 0 0 0 0 0 0 0 1201 3605 9453 28380 https://usegalaxy.eu/published/workflow?id=65aed668233d5f73
ucsc_axtchain ucsc_axtchain Chain together genome alignments 2024-08-26 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-axtchain 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 11 11 0 0 0 0 0 0 0 0 1 3 11 33
ucsc_axttomaf ucsc_axtomaf Convert dataset from axt to MAF format. 2024-08-27 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-axttomaf 469 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 12 12 0 0 0 0 0 0 0 0 1 3 12 36
ucsc_blat ucsc_blat Standalone blat sequence search command line tool 2017-05-17 http://genome.ucsc.edu/goldenPath/help/blatSpec.html 481 ucsc-blat 481 Up-to-date Sequence Analysis Sequence alignment Sequence alignment Sequence analysis Sequence analysis yating-l https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat blat BLAT Fast, accurate spliced alignment of DNA sequences. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ucsc_chainantirepeat ucsc_chainantirepeat Remove repeated chains 2025-03-07 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-chainantirepeat 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainantirepeat https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainantirepeat UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ucsc_chainnet ucsc_chainnet Make alignment nets out of chains 2024-08-30 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-chainnet 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 14 14 0 0 0 0 0 0 0 0 1 3 14 42
ucsc_chainprenet ucsc_chainprenet Remove chains that don't have a chance of being netted 2024-08-27 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-chainprenet 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 13 13 0 0 0 0 0 0 0 0 1 3 13 39
ucsc_chainsort ucsc_chainsort Sort chains. By default sorts by score. 2024-08-26 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-chainsort 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 13 13 0 0 0 0 0 0 0 0 1 3 13 39
ucsc_fasplit fasplit faSplit is a tool to split a single FASTA file into several files 2017-09-08 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-fasplit 469 Up-to-date Fasta Manipulation Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 503 529 3473 3613 666 668 7004 7037 197 197 1305 1305 5 5 9 9 1371 4141 11791 35546 https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.org.au/published/workflow?id=8ae08ac9e73c8241
ucsc_fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs 2023-01-11 http://hgdownload.cse.ucsc.edu/admin/exe/ 473 ucsc-fatovcf 473 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 62 62 473 473 150 150 770 770 6 6 108 108 0 0 0 0 218 654 1351 4053 variant-analysis/pox-tiled-amplicon
ucsc_maftoaxt maftoaxt Convert dataset from MAF to axt format 2024-07-30 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-maftoaxt 469 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 9 9 0 0 0 0 0 0 0 0 2 6 9 27
ucsc_netfilter ucsc_netfilter Filter out parts of net 2024-09-18 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-netfilter 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 9 9 0 0 0 0 0 0 0 0 1 3 9 27
ucsc_netsyntenic ucsc_netsyntenic Add synteny info to a net dataset 2024-09-04 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-netsyntenic 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 23 23 0 0 0 0 0 0 0 0 2 6 23 69
ucsc_nettoaxt ucsc_nettoaxt Convert net (and chain) to axt format. 2024-09-19 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-nettoaxt 469 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 8 8 0 0 0 0 0 0 0 0 1 3 8 24
ucsc_twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA 2016-08-19 https://genome.ucsc.edu/goldenpath/help/twoBit.html 472 ucsc-twobittofa 472 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 90 126 460 570 149 150 820 822 2 2 42 42 0 0 0 0 241 760 1322 4078
ucsc_wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig 2024-01-14 https://genome.ucsc.edu/goldenPath/help/bigWig.html 482 ucsc-wigtobigwig 482 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 204 204 3169 3169 447 447 5274 5274 36 36 435 435 0 0 0 0 687 2061 8878 26634 https://usegalaxy.eu/published/workflow?id=489926f9299594fe, https://usegalaxy.eu/published/workflow?id=4ca06bc64bf896a3, https://usegalaxy.eu/published/workflow?id=bffeb3cd0c708441, https://usegalaxy.eu/published/workflow?id=c46345ba876d5bfe
umi-tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq 2017-08-09 https://github.com/CGATOxford/UMI-tools 1.1.6 umi_tools 1.1.6 Up-to-date Sequence Analysis, Transcriptomics, Single Cell Sequencing quality control Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Sequence sites, features and motifs, Quality affairs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. 5 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 3 5 5 0 1126 1318 56600 71181 1032 1033 10626 10628 190 190 14499 14499 8 8 44 44 2356 7261 81769 259890 https://dev.workflowhub.eu/workflows/1214?version=1, https://dev.workflowhub.eu/workflows/1285?version=2, https://dev.workflowhub.eu/workflows/1397?version=1, https://usegalaxy.eu/published/workflow?id=06fe33c4420906bf, https://usegalaxy.eu/published/workflow?id=0821ec1cb4d6f30b, https://usegalaxy.eu/published/workflow?id=08cfb9b21c1ec808, https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=26185e8fa5a9b988, https://usegalaxy.eu/published/workflow?id=44c5999436da5f1e, https://usegalaxy.eu/published/workflow?id=49073a24429d93d6, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=a1e09c648d8f1fc7, https://usegalaxy.eu/published/workflow?id=af7c349497a75314, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=c64b219b4031fabd, https://usegalaxy.eu/published/workflow?id=c6b22fc33b569c8f, https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765, https://usegalaxy.eu/published/workflow?id=d4b3da4cc5a50044, https://usegalaxy.eu/published/workflow?id=d7aa4c258e2edc95, https://usegalaxy.eu/published/workflow?id=edbdbe7aa21ceba0, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://usegalaxy.eu/published/workflow?id=f841e1207611f28f, https://usegalaxy.org.au/published/workflow?id=7ae06a27188b9438, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org/published/workflow?id=b1b75a9323d25085 single-cell/scrna-preprocessing, single-cell/scrna-umis, transcriptomics/clipseq
unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. 2017-05-08 https://github.com/rrwick/Unicycler 0.5.1 unicycler 0.5.1 Up-to-date Assembly Genome assembly, Aggregation Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Microbiology, Genomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 4157 4473 76735 83979 5452 8063 61814 95623 2194 2298 19779 22043 226 226 1516 1516 12029 39118 159844 522849 https://dev.workflowhub.eu/workflows/1000?version=1, https://dev.workflowhub.eu/workflows/1107?version=1, https://dev.workflowhub.eu/workflows/1132?version=2, https://dev.workflowhub.eu/workflows/1182?version=2, https://dev.workflowhub.eu/workflows/1197?version=2, https://dev.workflowhub.eu/workflows/39?version=1, https://usegalaxy.eu/published/workflow?id=165089132248a0b0, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=346b46e6316c6950, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=7b755497d168cb13, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b2dfa74f55a73409, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=c702c76cadebac30, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e8eb80ee09159bac, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.fr/published/workflow?id=5bb882218afda132, https://usegalaxy.org.au/published/workflow?id=38d992baf9a2a2bc, https://usegalaxy.org.au/published/workflow?id=8f7d5ebead46a6d0, https://usegalaxy.org.au/published/workflow?id=9c60b83feaa22415, https://usegalaxy.org.au/published/workflow?id=b59fada651043735, https://usegalaxy.org.au/published/workflow?id=b7aa22291322e505, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org.au/published/workflow?id=f01be6a7685ac476, https://usegalaxy.org.au/published/workflow?id=fc3c83b11f527977, https://usegalaxy.org/published/workflow?id=5039ae2c81d0aba8, https://usegalaxy.org/published/workflow?id=69514a75e4c9af08, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=a67afbea4b2eb26b, https://usegalaxy.org/published/workflow?id=b43b72dcf5f7694d, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=db0671862a57968d, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/52?version=1, https://workflowhub.eu/workflows/68?version=1 assembly/assembly-with-preprocessing, assembly/unicycler-assembly, microbiome/plasmid-metagenomics-nanopore
upsetplot rcx_upsetplot Upset plot visualization tool using UpSetR 2025-04-17 https://github.com/galaxyproject/tools-iuc 1.4.0 r-upsetr 1.0.3 To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/upsetr https://github.com/galaxyproject/tools-iuc/tree/main/tools/upsetr 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
usher usher_matutils, usher UShER toolkit wrappers 2021-05-11 https://github.com/yatisht/usher 0.2.1 usher 0.6.3 To update Phylogenetics Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics Cladistics, Genotype and phenotype, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 5 5 1060 1060 0 0 0 0 0 0 0 0 0 0 0 0 5 15 1060 3180
valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. 2017-11-16 https://github.com/marbl/VALET valet 1.0 To update Metagenomics Sequence assembly, Sequence assembly visualisation Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly Metagenomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 74 94 485 696 71 71 242 242 0 0 0 0 0 0 0 0 145 455 727 2392 https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09
vapor vapor Classify Influenza samples from raw short read sequence data 2022-08-24 https://github.com/connor-lab/vapor 1.0.2 vapor 1.0.2 Up-to-date Sequence Analysis Data retrieval, De-novo assembly, Read mapping Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Whole genome sequencing, Mapping, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 157 157 71831 71831 22 22 708 708 0 0 0 0 0 0 0 0 179 537 72539 217617 https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=bc5ced57e711acf9, https://workflowhub.eu/workflows/1260?version=1 variant-analysis/aiv-analysis
vardict_java vardict_java VarDict - calls SNVs and indels for tumour-normal pairs 2020-08-21 https://github.com/AstraZeneca-NGS/VarDictJava 1.8.3 python To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 39 39 387 387 0 0 0 0 0 0 0 0 0 0 0 0 39 117 387 1161 https://workflowhub.eu/workflows/517?version=1, https://workflowhub.eu/workflows/518?version=1
variant_analyzer mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data 2019-11-20 2.0.0 matplotlib To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14 14 86 95 73 73 536 557 0 0 0 0 0 0 0 0 87 261 622 1896
varscan varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data 2018-07-10 https://dkoboldt.github.io/varscan/ 2.4.3 varscan 2.4.6 To update Variant Analysis iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 3 3 3 0 1467 1688 10551 12161 3638 3643 18710 18756 107 107 1239 1239 318 318 951 951 5530 16816 31451 96009 https://dev.workflowhub.eu/workflows/1081?version=1, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=231a2dc7412d250b, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=462582bbc236cb7b, https://usegalaxy.eu/published/workflow?id=4f62794453f65cba, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=83049910e2cd5128, https://usegalaxy.eu/published/workflow?id=88064e2231165fd2, https://usegalaxy.eu/published/workflow?id=a4e3667f6879bfaf, https://usegalaxy.eu/published/workflow?id=af30010868c97316, https://usegalaxy.org/published/workflow?id=0ee0493f3168cbb3, https://usegalaxy.org/published/workflow?id=18c6e87a884fb5ed, https://usegalaxy.org/published/workflow?id=3dbe754882a263cd, https://usegalaxy.org/published/workflow?id=4cbb8181cfdf55d9, https://usegalaxy.org/published/workflow?id=7c5e8394ce29288d, https://usegalaxy.org/published/workflow?id=bf90f2bd20fbff21, https://workflowhub.eu/workflows/36?version=1, https://workflowhub.eu/workflows/628?version=1 variant-analysis/somatic-variants
varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses 2024-01-27 https://github.com/jonas-fuchs/varVAMP/ 1.2.2 varvamp 1.2.2 Up-to-date Sequence Analysis PCR primer design PCR primer design Virology, Probes and primers Virology, Probes and primers iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 438 438 0 0 0 0 0 0 0 0 0 0 0 0 21 63 438 1314 sequence-analysis/viral_primer_design
vcf2maf vcf2maf vcf2maf: Convert VCF into MAF 2022-06-28 https://github.com/mskcc/vcf2maf 1.6.21 vcf2maf 1.6.22 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 53 53 1411 1411 0 0 0 0 5 5 87 87 0 0 0 0 58 174 1498 4494 https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1
vcf2tsv vcf2tsv Converts VCF files into tab-delimited format 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis, Convert Formats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 885 961 171548 172727 1093 2700 15916 43209 173 179 3405 3468 73 73 254 254 2224 8361 191123 601904 https://dev.workflowhub.eu/workflows/1100?version=2, https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31, https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb, https://usegalaxy.eu/published/workflow?id=3d8aa05129e44fdf, https://usegalaxy.eu/published/workflow?id=4d80a87510b2a54e, https://usegalaxy.eu/published/workflow?id=5a16af00bf8bf57b, https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8, https://usegalaxy.eu/published/workflow?id=a2d4221ad117c378, https://usegalaxy.org.au/published/workflow?id=2362ff8880213586, https://usegalaxy.org.au/published/workflow?id=3e6f755ee62f7301, https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886, https://usegalaxy.org/published/workflow?id=3d5347f1e8ee7db2, https://usegalaxy.org/published/workflow?id=415c7152cb78e86f, https://usegalaxy.org/published/workflow?id=43861b38cf6e927e, https://usegalaxy.org/published/workflow?id=4dbac8374419d29e, https://usegalaxy.org/published/workflow?id=4ed9f54caa932479, https://usegalaxy.org/published/workflow?id=50206b10de958d03, https://usegalaxy.org/published/workflow?id=57cfc1b5d9ea0d72, https://usegalaxy.org/published/workflow?id=5cad854edbbd3b69, https://usegalaxy.org/published/workflow?id=68d41ffbf92b2a8e, https://usegalaxy.org/published/workflow?id=a1047ce36ac8f871, https://usegalaxy.org/published/workflow?id=bb16936081b820f6, https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72 variant-analysis/baculovirus-isolate-variation, variant-analysis/non-dip
vcfaddinfo vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 32 875 888 35 115 6513 9000 7 7 181 206 0 0 0 0 72 298 7569 25232
vcfallelicprimitives vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 912 1273 5047 18602 1242 2023 7569 14895 208 240 2162 2251 3 3 5 5 2365 8269 14783 65319 https://dev.workflowhub.eu/workflows/1104?version=1, https://usegalaxy.eu/published/workflow?id=2f1ee01aeee2b9f0, https://usegalaxy.eu/published/workflow?id=4a89ddab941c6819, https://usegalaxy.eu/published/workflow?id=a4e3667f6879bfaf, https://usegalaxy.eu/published/workflow?id=ad609d1a3de251f5, https://usegalaxy.eu/published/workflow?id=b02d90c32dc67730, https://usegalaxy.eu/published/workflow?id=ffe93ec81afefd09, https://usegalaxy.org.au/published/workflow?id=1a159863e9d977a0, https://usegalaxy.org.au/published/workflow?id=738c0e8227519c25, https://usegalaxy.org.au/published/workflow?id=ac89c2d51c32cc9c, https://usegalaxy.org/published/workflow?id=70dacee3da375e2b, https://workflowhub.eu/workflows/35?version=1, https://workflowhub.eu/workflows/36?version=1 variant-analysis/dip
vcfanno vcfanno Annotate VCF files 2021-01-17 https://github.com/brentp/vcfanno 0.3.5 vcfanno 0.3.5 Up-to-date Variant Analysis SNP annotation SNP annotation Genetic variation, Data submission, annotation and curation Genetic variation, Data submission, annotation and curation iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 190 190 1187 1187 0 0 0 0 0 0 0 0 0 0 0 0 190 570 1187 3561 https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1
vcfannotate vcfannotate Intersect VCF records with BED annotations 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 158 187 2819 2887 668 1457 3632 14750 63 67 642 673 5 5 6 6 894 3504 7099 32514 https://usegalaxy.org.au/published/workflow?id=142e5f7c1f340838, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org/published/workflow?id=3e2bbafb8c6580af
vcfannotategenotypes vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 64 70 186 210 150 397 474 1843 11 11 190 218 1 1 3 3 226 931 853 3980
vcfbedintersect vcfbedintersect Intersect VCF and BED datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 192 221 3123 4225 428 1209 4828 20678 43 45 536 588 2 2 7 7 665 2807 8494 42486 https://usegalaxy.org/published/workflow?id=6da54816b436dc58, https://usegalaxy.org/published/workflow?id=9b81d47a468d6f99
vcfbreakcreatemulti vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34 40 399 478 79 314 3952 10504 8 8 374 420 1 1 1 1 122 607 4726 20855 https://usegalaxy.org/published/workflow?id=df6c398b2d4f1e99
vcfcheck vcfcheck Verify that the reference allele matches the reference genome 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 103 114 1607 1637 220 645 795 1934 16 17 248 279 1 1 1 1 340 1457 2651 9153 https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a
vcfcombine vcfcombine Combine multiple VCF datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 310 539 1510 2177 1074 2808 4745 19984 65 67 500 544 5 5 9 9 1454 6327 6764 36242 https://usegalaxy.eu/published/workflow?id=a2d4221ad117c378, https://usegalaxy.eu/published/workflow?id=ddd604341afd9cf7, https://usegalaxy.org/published/workflow?id=2478426a119d9d93, https://usegalaxy.org/published/workflow?id=2d44e2b020bf94f8, https://usegalaxy.org/published/workflow?id=865d2cc4d14ec7e1, https://usegalaxy.org/published/workflow?id=c4a1246974f279c5, https://usegalaxy.org/published/workflow?id=d3e656ab45f40c11, https://usegalaxy.org/published/workflow?id=d43b771d93f0f609, https://usegalaxy.org/published/workflow?id=e2432c4d2b61705a
vcfcommonsamples vcfcommonsamples Output records belonging to samples commong between two datasets. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 36 44 226 258 79 291 248 1877 10 12 199 235 3 3 15 15 128 606 688 3761
vcfdistance vcfdistance Calculate distance to the nearest variant. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 92 95 559 589 139 307 2019 2446 20 23 275 312 2 2 2 2 253 933 2855 9059
vcffilter vcffilter2 Tool for filtering VCF files 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2411 2578 39849 50186 5825 11121 74909 167761 342 360 3198 3356 51 51 200 200 8629 31368 118156 457815 https://dev.workflowhub.eu/workflows/1100?version=2, https://usegalaxy.eu/published/workflow?id=22454322d370b3ff, https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb, https://usegalaxy.eu/published/workflow?id=2a13eb981d6ee36e, https://usegalaxy.eu/published/workflow?id=3b7c0b64033f38ac, https://usegalaxy.eu/published/workflow?id=533819bcb5aa78c5, https://usegalaxy.eu/published/workflow?id=591ebf913450f49e, https://usegalaxy.eu/published/workflow?id=5a16af00bf8bf57b, 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vcffixup vcffixup Count the allele frequencies across alleles present in each record in the VCF file. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 161 182 904 993 316 1009 2273 5399 30 33 256 289 1 1 1 1 508 2241 3434 13550
vcfflatten vcfflatten2 Removes multi-allelic sites by picking the most common alternate 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 24 29 169 190 71 209 381 935 14 16 315 363 0 0 0 0 109 472 865 3218
vcfgeno2haplo vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 116 122 822 846 186 525 2410 3760 21 23 219 255 2 2 2 2 325 1322 3453 11769 https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a
vcfgenotypes vcfgenotypes Convert numerical representation of genotypes to allelic. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 138 152 1335 1438 261 877 3396 6399 22 24 226 258 1 1 6 6 422 1898 4963 18027
vcfhethom vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 213 221 2083 2143 195 658 1857 3877 24 27 580 664 2 2 10 10 434 1776 4530 15754
vcfleftalign vcfleftalign Left-align indels and complex variants in VCF dataset 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 42 47 676 725 87 296 346 1114 13 15 190 239 2 2 2 2 144 648 1214 4508 https://usegalaxy.org/published/workflow?id=2478426a119d9d93
vcfprimers vcfprimers Extract flanking sequences for each VCF record 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 34 571 712 68 204 368 854 11 13 196 237 1 1 3 3 106 464 1138 4082
vcfrandomsample vcfrandomsample Randomly sample sites from VCF dataset 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15 17 156 171 28 78 137 355 6 6 190 213 0 0 0 0 49 199 483 1705
vcfselectsamples vcfselectsamples Select samples from a VCF file 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 94 858 947 230 975 1221 6324 20 21 345 384 0 0 0 0 325 1740 2424 12503 https://usegalaxy.org/published/workflow?id=63e0dcf18794dbc1, https://usegalaxy.org/published/workflow?id=67e56a9919ed84f7, https://usegalaxy.org/published/workflow?id=9b4323b68f609e06, https://usegalaxy.org/published/workflow?id=ad6143e2f74e1e94, https://usegalaxy.org/published/workflow?id=db8443163482a2e0, https://usegalaxy.org/published/workflow?id=df6c398b2d4f1e99
vcfsort vcfsort Sort VCF dataset by coordinate 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 204 1857 1931 436 1334 13376 25333 77 83 567 722 3 3 70 70 705 3034 15870 59796 https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=d69a765cfc82a399, https://usegalaxy.org/published/workflow?id=50206b10de958d03, https://usegalaxy.org/published/workflow?id=bb16936081b820f6, https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72
vcfvcfintersect vcfvcfintersect Intersect two VCF datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 752 806 977259 977936 994 2200 65241 83694 236 241 21102 21158 15 15 1673 1673 1997 7256 1065275 3215011 https://dev.workflowhub.eu/workflows/143?version=1, https://dev.workflowhub.eu/workflows/196?version=2, https://usegalaxy.eu/published/workflow?id=0882300f7b399587, https://usegalaxy.eu/published/workflow?id=0be293debca8fb9b, https://usegalaxy.eu/published/workflow?id=2573209308aaad23, https://usegalaxy.eu/published/workflow?id=4b4bfc79205d83f1, https://usegalaxy.eu/published/workflow?id=52bdf400f97c5770, https://usegalaxy.eu/published/workflow?id=579dd1e95e76402f, https://usegalaxy.eu/published/workflow?id=6dbac47941a804da, https://usegalaxy.eu/published/workflow?id=a6f4371ef9bc1aab, https://usegalaxy.eu/published/workflow?id=ed20bd120064bab0, https://usegalaxy.eu/published/workflow?id=ee6dc47660540ba6, https://usegalaxy.eu/published/workflow?id=fc216dfb0ec9ed41, https://usegalaxy.eu/published/workflow?id=fcf745185d6e0ea4, https://usegalaxy.fr/published/workflow?id=7d27dd394b921846, https://usegalaxy.fr/published/workflow?id=98529cff0ef36b91, https://usegalaxy.fr/published/workflow?id=d0d12c0b80c286f9, https://usegalaxy.fr/published/workflow?id=e0b225d4b2556365, https://usegalaxy.org.au/published/workflow?id=094a545d44ce28cc, https://usegalaxy.org.au/published/workflow?id=2b2ce7e1206d177d, https://usegalaxy.org.au/published/workflow?id=3223ceaa2b58d940, https://usegalaxy.org.au/published/workflow?id=3c657dd766d02f6a, https://usegalaxy.org.au/published/workflow?id=52b6fe5af4911b1a, https://usegalaxy.org.au/published/workflow?id=7fd58f5fc93f414e, https://usegalaxy.org.au/published/workflow?id=810242a3dc4f6170, https://usegalaxy.org.au/published/workflow?id=888eb87b62c4e6dd, https://usegalaxy.org.au/published/workflow?id=baa763dbdf6afb71, https://usegalaxy.org.au/published/workflow?id=bcf230e526632064, https://usegalaxy.org.au/published/workflow?id=be9213411c520096, https://usegalaxy.org.au/published/workflow?id=c1ce3f2ae7c81c3e, https://usegalaxy.org.au/published/workflow?id=d35d05be576e8b13, https://usegalaxy.org.au/published/workflow?id=e439a0e17a90d24c, https://usegalaxy.org.au/published/workflow?id=fe5542c99cdc57ce, https://usegalaxy.org/published/workflow?id=21a047a4e068860f, https://usegalaxy.org/published/workflow?id=262ab42118016c41, https://usegalaxy.org/published/workflow?id=4cf8cc42e97b2da6, https://usegalaxy.org/published/workflow?id=6b11d738ee57f245, https://usegalaxy.org/published/workflow?id=7dde0721a382ea3e, https://usegalaxy.org/published/workflow?id=7e2651e5ed17e3db, https://usegalaxy.org/published/workflow?id=98b2ac8fc75781f8, https://usegalaxy.org/published/workflow?id=9b81d47a468d6f99, https://usegalaxy.org/published/workflow?id=9e487f763daa66c0, https://usegalaxy.org/published/workflow?id=9fc9f1db50019929, https://usegalaxy.org/published/workflow?id=a98a3ac1a41752bc, https://usegalaxy.org/published/workflow?id=b461ac6f18e0c9cf, https://usegalaxy.org/published/workflow?id=bd355e8ce58a139e, https://usegalaxy.org/published/workflow?id=bf3ccae8d5b6ef58, https://usegalaxy.org/published/workflow?id=d196c3bde666eccb, https://usegalaxy.org/published/workflow?id=d4ea6cdd40522eb1, https://usegalaxy.org/published/workflow?id=e282f505ba9f729f, https://usegalaxy.org/published/workflow?id=e2c77aeabb8053b4, https://usegalaxy.org/published/workflow?id=f9d546aae406cf15, https://workflowhub.eu/workflows/110?version=10
vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist 2015-08-27 https://cran.r-project.org/package=vegan 2.4-3 r-vegan 2.3_4 To update Metagenomics Standardisation and normalisation, Analysis Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science Ecology, Phylogenetics, Environmental science iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 199 217 2164 2328 432 765 3651 5713 0 0 0 0 0 0 0 0 631 2244 5815 19671
velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. 2021-04-30 http://velocyto.org/ 0.17.17 velocyto.py 0.17.17 Up-to-date Transcriptomics, Single Cell RNA-Seq analysis, Splicing analysis RNA-Seq analysis, Splicing analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto velocyto Velocyto Estimating RNA velocity in single cell RNA sequencing datasets 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 74 74 9 9 65 65 1 1 96 96 0 0 0 0 15 45 235 705 https://usegalaxy.eu/published/workflow?id=c5841e0458a4ebf7, https://usegalaxy.eu/published/workflow?id=c58bb47e04157ee6, https://usegalaxy.org.au/published/workflow?id=1e5a77d9e9630115, https://usegalaxy.org.au/published/workflow?id=77e0ca6492f40c9c, https://usegalaxy.org/published/workflow?id=29d51c37d66deeeb, https://usegalaxy.org/published/workflow?id=6592430b80345167
velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies 2020-06-09 https://www.ebi.ac.uk/~zerbino/velvet/ velvet 1.2.10 To update Assembly Formatting, De-novo assembly Formatting, De-novo assembly Sequence assembly Sequence assembly devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 4241 4743 25341 29448 8391 8391 53931 53931 3625 3694 29765 29920 142 142 628 628 16399 49768 109665 333257 https://dev.workflowhub.eu/workflows/1003?version=1, https://dev.workflowhub.eu/workflows/1192?version=2, https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=56edd22d14392691, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=b7c2440621968526, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.org.au/published/workflow?id=874492eb776ba813, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=9b75924c483b5f6b, https://usegalaxy.org.au/published/workflow?id=aee5b5645c51cac3, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org.au/published/workflow?id=fb0986a952c35e0a, https://usegalaxy.org/published/workflow?id=4e1ae78405034ad3, https://usegalaxy.org/published/workflow?id=51c485af11d90700, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=c30f6ca171896908, https://usegalaxy.org/published/workflow?id=e745c45651d829b8, https://usegalaxy.org/published/workflow?id=f926e70bee242785 assembly/general-introduction
velvetoptimiser velvetoptimiser Automatically optimize Velvet assemblies 2017-12-19 2.2.6+galaxy2 velvet 1.2.10 To update Assembly Optimisation and refinement, Sequence assembly Optimisation and refinement, Sequence assembly Genomics, Sequence assembly Genomics, Sequence assembly simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 937 1070 4635 5624 2338 2350 10295 10321 990 1423 3264 5686 0 0 0 0 4265 13373 18194 58019 https://dev.workflowhub.eu/workflows/1124?version=1, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.org.au/published/workflow?id=8abcfe166f1a6cd8, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8 assembly/debruijn-graph-assembly
verkko verkko Telomere-to-telomere assembly pipeline 2023-01-24 https://github.com/marbl/verkko 1.3.1 verkko 2.2.1 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 33 33 69 69 0 0 0 0 8 8 61 61 0 0 0 0 41 123 130 390
vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods 2020-04-08 https://github.com/vgteam/vg 1.23.0 vg 1.65.0 To update Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 18 18 479 479 0 0 0 0 0 0 0 0 0 0 0 0 18 54 479 1437 https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40
virannot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers 2024-03-04 https://github.com/marieBvr/virAnnot 1.2.0 biopython 1.70 To update Metagenomics Sequence annotation, Sequence clustering, Sequence cluster visualisation Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology Metagenomics, Virology, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot virannot virAnnot VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project "Plant Health Bioinformatics Network". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy. 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 29 271 271 0 0 0 0 0 0 0 0 4 4 14 14 33 99 285 855 https://usegalaxy.eu/published/workflow?id=86465932556bc96c
virheat virheat generates a heatmap of allele frequencies from vcf files 2024-05-15 https://github.com/jonas-fuchs/virHEAT 0.7.1 virheat 0.7.4 To update Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat virheat virHEAT VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 15 15 0 0 0 0 0 0 0 0 0 0 0 0 4 12 15 45
virhunter virhunter Deep Learning method for novel virus detection in sequencing data 2022-09-13 https://github.com/cbib/virhunter 1.0.0 numpy To update Machine Learning Sequence classification Sequence classification Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 760 760 0 0 0 0 0 0 0 0 0 0 0 0 97 291 760 2280
volcanoplot volcanoplot Tool to create a Volcano Plot 2018-10-01 https://ggplot2.tidyverse.org/ 3.5.2 r-ggplot2 2.2.1 To update Visualization, Transcriptomics, Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 4014 4259 36539 40056 6282 6282 61543 61543 941 947 7726 7854 193 193 1260 1260 11430 34541 107068 324849 https://dev.workflowhub.eu/workflows/1335?version=2, https://dev.workflowhub.eu/workflows/1395?version=1, https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=3ac10b9887fd0fb2, https://usegalaxy.eu/published/workflow?id=68e8042f11d5a3fd, https://usegalaxy.eu/published/workflow?id=7136ce9f18c74853, https://usegalaxy.eu/published/workflow?id=82ef590b5821805d, https://usegalaxy.eu/published/workflow?id=95c4d5549e820d88, https://usegalaxy.eu/published/workflow?id=a9469155eee12ff1, https://usegalaxy.eu/published/workflow?id=bc79a9f797334b01, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809, https://usegalaxy.eu/published/workflow?id=d1b3b62e7f91e217, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.eu/published/workflow?id=fd156028b09d213a, https://usegalaxy.org.au/published/workflow?id=28705b86e0595ded, https://usegalaxy.org.au/published/workflow?id=897e9d7432d231e9, https://usegalaxy.org.au/published/workflow?id=8eab5e2b2c683076, https://usegalaxy.org.au/published/workflow?id=a8d9a16eea69b812, https://usegalaxy.org.au/published/workflow?id=a9e59d38c6c710bc, https://usegalaxy.org/published/workflow?id=0930f955bdac93e8, https://usegalaxy.org/published/workflow?id=13a3954b8894e1b1, https://usegalaxy.org/published/workflow?id=25cdc47baba556c5, https://usegalaxy.org/published/workflow?id=420a332da24fb9e9, https://usegalaxy.org/published/workflow?id=4c840284d2984fa0, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=68832752b883c226, https://usegalaxy.org/published/workflow?id=7497bfdd2085b6e0, https://workflowhub.eu/workflows/1201?version=3, https://workflowhub.eu/workflows/1207?version=2 genome-annotation/crispr-screen, single-cell/pseudobulk-analysis, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-viz-with-volcanoplot, transcriptomics/rna-seq-viz-with-volcanoplot-r
vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. 2014-11-30 https://github.com/torognes/vsearch 2.8.3 vsearch 2.30.0 To update Sequence Analysis DNA mapping, Chimera detection DNA mapping, Chimera detection Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. 8 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 0 0 0 0 0 8 0 0 0 0 0 8 8 8 0 604 701 11607 12884 1036 2127 13254 56821 265 300 5716 6352 16 16 31 31 1921 6986 30608 137304 https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1
vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. 2020-04-26 https://github.com/USDA-VS/vSNP 3.0.6 pysam 0.23.2 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
weblogo3 rgweblogo3 Sequence Logo generator for fasta 2017-11-17 3.5.0 weblogo 3.7.9 To update Graphics Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis Nucleic acid sites, features and motifs, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 weblogo WebLogo Web-based application designed to make generate sequence logos. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 219 243 2807 2923 1346 3687 9506 30859 50 61 1261 1353 10 10 32 32 1625 7251 13606 62379 https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc
windowmasker windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker 2023-12-14 https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ 1.0 blast 2.16.0 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 34 812 812 17 17 558 558 6 6 532 532 0 0 0 0 57 171 1902 5706 https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=efb58bba65393347
winnowmap winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. 2021-04-29 https://github.com/marbl/Winnowmap 2.03 winnowmap 2.03 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 49 49 289 289 16 16 84 84 0 0 0 0 0 0 0 0 65 195 373 1119 https://usegalaxy.eu/published/workflow?id=2cd5670f075704ab, https://usegalaxy.eu/published/workflow?id=e522be58f0bac656
xpath xpath XPath XML querying tool 2015-04-14 http://search.cpan.org/dist/XML-XPath/ perl-xml-xpath 1.47 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8 9 99 236 0 1 0 1 0 0 0 0 0 0 0 0 8 26 99 435 https://usegalaxy.eu/published/workflow?id=1f3f6757de60d3cf
yahs yahs Yet Another Hi-C scaffolding tool 2022-06-28 https://github.com/c-zhou/yahs 1.2a.2 yahs 1.2.2 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 210 210 751 751 74 74 399 399 26 26 779 779 0 0 0 0 310 930 1929 5787 https://usegalaxy.eu/published/workflow?id=069d99391a69baf4, https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920, https://usegalaxy.eu/published/workflow?id=3010ecad1a342331, https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f, https://usegalaxy.eu/published/workflow?id=3b57fc81001667b5, https://usegalaxy.eu/published/workflow?id=4949751217c0e211, https://usegalaxy.eu/published/workflow?id=652433160b04b232, https://usegalaxy.eu/published/workflow?id=792b24fc23bd3071, https://usegalaxy.eu/published/workflow?id=a37d1e0db16cfb67, https://usegalaxy.eu/published/workflow?id=a53f78aa6866b811, https://usegalaxy.eu/published/workflow?id=b287bb779cf686ef, https://usegalaxy.eu/published/workflow?id=bc8ccd13a07bd9ec, https://usegalaxy.eu/published/workflow?id=c8f94a2e838fc0f1, https://usegalaxy.eu/published/workflow?id=feeb1fa358ccf328, https://usegalaxy.org.au/published/workflow?id=0aa316f8c6cff444, https://usegalaxy.org.au/published/workflow?id=0dbb85f727302a72, https://usegalaxy.org.au/published/workflow?id=29f0c07c8a24b542, https://usegalaxy.org.au/published/workflow?id=455e68f185fec41b, https://usegalaxy.org.au/published/workflow?id=6c1c11a81a2ab1b8, https://usegalaxy.org.au/published/workflow?id=6ec5728eec9c26d7, https://usegalaxy.org.au/published/workflow?id=7028436ef03171cc, https://usegalaxy.org.au/published/workflow?id=77b2fcf8c805ad5d, https://usegalaxy.org.au/published/workflow?id=7a97e8ccc332c1e8, https://usegalaxy.org.au/published/workflow?id=86eb0ea9dc230f04, https://usegalaxy.org.au/published/workflow?id=ae6a03240680712a, https://usegalaxy.org.au/published/workflow?id=b9e89401313a0cca, https://usegalaxy.org.au/published/workflow?id=be35847680078c90, https://usegalaxy.org.au/published/workflow?id=cac0b8a09d59044b, https://usegalaxy.org.au/published/workflow?id=fdec6e2fcd5e2cf5, https://usegalaxy.org/published/workflow?id=155839aeb6340f54, https://usegalaxy.org/published/workflow?id=28dbbfb3d480f4b1, https://usegalaxy.org/published/workflow?id=28ddea356ae57da1, https://usegalaxy.org/published/workflow?id=3d805d7e0f34c727, https://usegalaxy.org/published/workflow?id=3db51822f04f4ff7, https://usegalaxy.org/published/workflow?id=6341c384ceaf47ed, https://usegalaxy.org/published/workflow?id=88327cb2e0fe3c25, https://usegalaxy.org/published/workflow?id=903e35b62946ed76, https://usegalaxy.org/published/workflow?id=9f4c4038d1c519e2, https://usegalaxy.org/published/workflow?id=a4a6d6846c1692f9, https://usegalaxy.org/published/workflow?id=afa89bb0e8966753, https://workflowhub.eu/workflows/1054?version=1, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/625?version=13, https://workflowhub.eu/workflows/702?version=1 assembly/vgp_genome_assembly
zerone zerone ChIP-seq discretization and quality control 2018-09-05 https://github.com/nanakiksc/zerone 1.0 zerone 1.0 Up-to-date ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8 12 63 96 0 0 0 0 0 0 0 0 0 0 0 0 8 28 63 222
CRSConverter crsconverter Tools to transforms geographical vector data to a specified coordinate reference system. 2025-05-20 https://github.com/Morphy427/phylodiversity_workflow/CRSConverter 1.1 r-sf To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/CRSConverter 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
EstimEndem estimate_endem Tools to estimates the endemism of each cell in a spatial grid. 2025-05-20 https://github.com/Morphy427/phylodiversity_workflow/EstimEndem 0.1.1+galaxy0 r-phyloregion To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/EstimEndem 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Geometric means (Dead wood) Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). 2023-11-10 https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom 0.1.0+galaxy0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 30 72 72 0 0 0 0 0 0 0 0 1 1 17 17 31 93 89 267
MALDIquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. 2018-08-22 http://strimmerlab.org/software/maldiquant/ 1.22.0 r-base To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 60 69 1227 3827 0 0 0 0 40 40 1213 1213 0 0 0 0 100 309 2440 9920 https://dev.workflowhub.eu/workflows/1123?version=1, https://usegalaxy.eu/published/workflow?id=7ee6976f69131683, https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73, https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89 metabolomics/msi-finding-nglycans
MFAssignR mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements 2024-08-02 https://github.com/RECETOX/MFAssignR 1.1.2 r-mfassignr 1.1.2 Up-to-date Metabolomics Visualisation Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows Proteomics experiment, Molecular interactions, pathways and networks, Workflows recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr mfassignr MFAssignR Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements. 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 23 50 50 0 0 0 0 0 0 0 0 0 0 0 0 23 69 50 150 metabolomics/mfassignr
Make data paper sketches from EML data_paper_from_EML This tool derived from the R Shiny App MetaShRIMPS <https://github.com/TanguyGen/metaCure> is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. 2024-10-15 https://github.com/TanguyGen/emldown 0.1.0+galaxy0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 24 24 0 0 0 0 0 0 0 0 0 0 0 0 3 9 24 72
PylOccuMatcher phylogenetic_occupancy_matcher Tools to matches phylogenetic data with occupancy data. 2025-05-20 https://github.com/Morphy427/phylodiversity_workflow/PhylOccuMatcher 1.0 r-phyloregion To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/PhylOccuMatcher 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
PyloIndex phylo_index Tools to computes the phylodiversity index. 2025-05-20 https://github.com/Morphy427/phylodiversity_workflow/PyloIndex 1.0 r-phyloregion To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/PhyloIndex 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
QCxMS qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). 2023-08-24 https://github.com/grimme-lab/QCxMS 5.2.1 To update Computational chemistry, Molecular Dynamics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 20 35682 35682 0 0 0 0 6 6 678 678 0 0 0 0 26 78 36360 109080 https://dev.workflowhub.eu/workflows/1367?version=1, https://usegalaxy.eu/published/workflow?id=4e9a2e12467bc02e, https://usegalaxy.eu/published/workflow?id=5465916d9b51f411, https://workflowhub.eu/workflows/897?version=2 metabolomics/qcxms-predictions
SCCAF run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. 2019-10-20 https://github.com/sccaf/sccaf 0.0.9 sccaf 0.0.10 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 103 110 1 1 1 1 0 0 0 0 0 0 0 0 20 60 104 319
WormsMeasurements WormsMeasurements This tool uses WoRMS (World Register of Marine Species) to add measurement values to a dataset based on scientific names. 2025-05-07 https://github.com/jeanlecras/tools-ecology 0.1.2 r-base To update Ecology ecology https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements https://github.com/galaxyecology/tools-ecology/tree/master/tools/WormsMeasurements 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ecology/ecoregiolifetraits
ab1fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files 2021-10-08 1.20.0 bioconductor-sangerseqr 1.42.0 To update Convert Formats ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 346 346 55863 55863 0 0 0 0 0 0 0 0 16 16 6494 6494 362 1086 62357 187071 https://dev.workflowhub.eu/workflows/1287?version=2, https://dev.workflowhub.eu/workflows/1292?version=2, https://usegalaxy.eu/published/workflow?id=52cb9bacc26b013e, https://usegalaxy.eu/published/workflow?id=c7f34c67c9054234, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a ecology/ENA_Biodiv_submission, sequence-analysis/Manage_AB1_Sanger
ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. 2019-06-13 http://ambermd.org/AmberTools.php 21.10 ambertools To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 7 2 7 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 5 0 577 579 42750 42972 199 199 1519 1519 103 103 1991 1991 0 0 0 0 879 2639 46260 139002 https://dev.workflowhub.eu/workflows/1134?version=1, https://usegalaxy.eu/published/workflow?id=07e1478df88a17cc, https://usegalaxy.eu/published/workflow?id=2a1b21d39ebb6e49, https://usegalaxy.eu/published/workflow?id=3729015f676693c8, https://usegalaxy.eu/published/workflow?id=3c6ff60d1d3ceb3d, https://usegalaxy.eu/published/workflow?id=5d793801998146bc, https://usegalaxy.eu/published/workflow?id=843c10c447496280, https://usegalaxy.eu/published/workflow?id=84c95f31896213fd, https://usegalaxy.eu/published/workflow?id=abd1cb3457338eb5, https://usegalaxy.eu/published/workflow?id=adc6d049e9283789, https://usegalaxy.eu/published/workflow?id=bf99d06567288766, https://usegalaxy.eu/published/workflow?id=c39a79bb45b2566e, https://usegalaxy.eu/published/workflow?id=d4d8e907e26c8587, https://usegalaxy.eu/published/workflow?id=e0dddc2579c3614e, https://usegalaxy.eu/published/workflow?id=e73beff62f35d677, https://usegalaxy.org.au/published/workflow?id=28cf646b95e4d3ab, https://usegalaxy.org/published/workflow?id=00a4dbc9329c638b, https://usegalaxy.org/published/workflow?id=0fb89e9c397c8938, https://usegalaxy.org/published/workflow?id=183254b3565bcb04, https://usegalaxy.org/published/workflow?id=3c1e2bbb1a77cc30, https://usegalaxy.org/published/workflow?id=442a2868873e7f77, https://usegalaxy.org/published/workflow?id=a638e12411586555, https://usegalaxy.org/published/workflow?id=aaec757e04605d3a, https://usegalaxy.org/published/workflow?id=ad19db6504b6dc33, https://workflowhub.eu/workflows/247?version=2, https://workflowhub.eu/workflows/248?version=4, https://workflowhub.eu/workflows/761?version=1, https://workflowhub.eu/workflows/762?version=1, https://workflowhub.eu/workflows/763?version=1, https://workflowhub.eu/workflows/764?version=1 computational-chemistry/htmd-analysis
appendfdr append_fdr 2015-01-24 0.2.0 To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. 2024-05-14 https://github.com/AquaINFRA/galaxy 1.0 To update Ecology ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 36 36 277 277 0 0 0 0 0 0 0 0 0 0 0 0 36 108 277 831
aquainfra_ogc_api_processes aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. 2024-10-10 https://github.com/AquaINFRA/galaxy 0.6.0 r-base To update Ecology ecology https://github.com/AquaINFRA/tools-ecology/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 257 257 0 0 0 0 0 0 0 0 0 0 0 0 26 78 257 771
artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis 2020-10-02 http://artbio.fr 1.10+galaxy0 samtools 1.22 To update SAM, Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
astronomicalarchivestool astronomical_archives Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy 2023-07-17 0.10.2 astropy To update Data Source astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/ https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 55 55 0 0 0 0 0 0 0 0 0 0 0 0 7 21 55 165
astropytools astropy_csv2fits, astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo AstropyTools library contains Galaxy tools for elementary Astrophysical operations 2023-04-11 https://github.com/astropy/astropy 0.1.0+galaxy0 astropy To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 5 5 13 13 0 0 0 0 0 0 0 0 0 0 0 0 5 15 13 39 https://usegalaxy.eu/published/workflow?id=d9535e4afec8866b, https://workflowhub.eu/workflows/1267?version=1
atlas_fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. 2022-03-09 https://github.com/ebi-gene-expression-group/atlas-fastq-provider 0.4.4 atlas-fastq-provider 0.4.7 To update Data Source, RNA, Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bamparse bamparse Generates hit count lists from bam alignments. 2017-10-12 http://artbio.fr 4.1.1 pysam 0.23.2 To update RNA, Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
baseline_toxicity_calculator tt_baseline Toxicity prediction using QSAR models 2024-03-25 https://github.com/bernt-matthias/mb-galaxy-tools 0.1.0+galaxy0 pandas To update Ecology, Text Manipulation mbernt https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bed_to_protein_map bed_to_protein_map Converts a BED file to a tabular list of exon locations 2018-01-04 0.2.0 python To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 135 142 409 440 104 104 373 373 14 14 180 180 0 0 0 0 253 766 962 2917 https://dev.workflowhub.eu/workflows/1042?version=1, https://dev.workflowhub.eu/workflows/1201?version=2, https://dev.workflowhub.eu/workflows/1386?version=1, https://dev.workflowhub.eu/workflows/1398?version=1, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474 proteomics/neoantigen-2-non-reference-database-generation, proteomics/proteogenomics-dbcreation
bgc_ocean harmonize_insitu_to_netcdf Process in-situ and biogechemical oceanographic Argo or Glider data for the Earth System 2024-12-05 https://github.com/Marie59/FE-ft-ESG/tree/main/ocean 2.0 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 19 19 0 0 0 0 0 0 0 0 0 0 0 0 2 6 19 57
bigwig_to_bedgraph bigwig_to_bedgraph Converts a bigWig file to bedGraph format 2021-10-06 http://artbio.fr 377+galaxy1 ucsc-bigwigtobedgraph 469 To update Convert Formats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 641 753 6696 7952 0 0 0 0 0 1 0 3 0 0 0 0 641 2036 6696 21347
bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format 2018-09-25 https://artbio.fr 3+galaxy0 ucsc-bigwiginfo 469 To update Convert Formats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. 2018-10-03 http://thegrantlab.org/bio3d/index.php 2.4_1 r-bio3d 2.3_3 To update Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 5 4 5 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 1266 1297 11824 12101 294 294 1162 1162 238 238 3022 3022 0 0 0 0 1798 5425 16008 48301 https://dev.workflowhub.eu/workflows/1062?version=1, https://dev.workflowhub.eu/workflows/1122?version=1, https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=9858fdf13a522ea8, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0, https://usegalaxy.org.au/published/workflow?id=c2f25a1bf07e8ab1 computational-chemistry/analysis-md-simulations, computational-chemistry/htmd-analysis
biobb_pytorch biobb_pytorch_apply_mdae, biobb_pytorch_train_mdae biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular [PyTorch](https://pytorch.org/) Python library. 2024-06-26 https://github.com/bioexcel/biobb_pytorch 4.2.1 biobb_pytorch 5.0.0 To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biobb_pytorch https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biobb_pytorch 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bioconductor-msnbase bioconductor_msnbase_centroid, bioconductor_msnbase_smooth_chromatogram, bioconductor_msnbase_smooth_mz MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. 2025-01-22 https://bioconductor.org/packages/release/bioc/html/MSnbase.html 2.32.0 bioconductor-msnbase 2.32.0 Up-to-date Metabolomics, Proteomics Data handling, Visualisation Data handling, Visualisation Proteomics, Proteomics experiment, Data management, Data visualisation Proteomics, Proteomics experiment, Data visualisation recetox https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-msnbase https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-msnbase msnbase MSnbase Basic plotting, data manipulation and processing of MS-based Proteomics data. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bioconductor_scp bioconductor_scp scp is a package for the single cell proteomics data processing. 2025-01-21 https://uclouvain-cbio.github.io/scp/index.html 1.16.0 bioconductor-scp 1.16.0 Up-to-date Proteomics, Single Cell Visualisation, Expression analysis Visualisation, Expression analysis Proteomics experiment, Proteomics Proteomics experiment, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp scp scp Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 proteomics/bioconductor-scp
biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis 2020-01-30 https://github.com/moldyn/ 1.5.2 scipy To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 130 130 550 550 165 165 557 557 0 0 0 0 0 0 0 0 295 885 1107 3321 https://usegalaxy.eu/published/workflow?id=1b10ece62e745125, https://usegalaxy.eu/published/workflow?id=d1357759d0962144, https://usegalaxy.eu/published/workflow?id=e3b0b521ee8f2aef, https://usegalaxy.org/published/workflow?id=195a608c481040de, https://usegalaxy.org/published/workflow?id=28c7e8269d478244, https://usegalaxy.org/published/workflow?id=634bbef1f67a0e30, https://workflowhub.eu/workflows/249?version=2
biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. 2020-08-26 https://bitbucket.org/djoumbou/biotransformerjar/src/master/ 3.0.20230403 biotransformer 3.0.20230403 Up-to-date Metabolomics Metabolic pathway prediction, PTM site prediction, Natural product identification Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 67 67 0 0 0 0 1 3 67 201
blast2go blast2go Maps BLAST results to GO annotation terms 2013-09-23 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe To update Ontology Manipulation, Sequence Analysis Gene functional annotation Gene functional annotation Nucleic acid sites, features and motifs Nucleic acid sites, features and motifs peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Blast2GO Blast2GO Bioinformatics platform for high-quality functional annotation and analysis of genomic datasets. It allows analyzing and visualizing newly sequenced genomes by combining state-of-the-art methodologies, standard resources and algorithms. It allows to gain biological insights fast and easy even for completely novel genomes. Perform out-of-the-box the entire workflow of functional annotation of your transcriptomic datasets including its analysis and biological interpretation. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 235 301 977 1238 0 0 0 0 0 0 0 0 1 1 3 10 236 774 980 3208 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a
blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option 2015-01-24 https://blast.ncbi.nlm.nih.gov/ 2.6.0 blast 2.16.0 To update Sequence Analysis galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files 2014-05-15 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 To update Fasta Manipulation, Sequence Analysis Gene functional annotation, Nucleic acid sequence analysis Gene functional annotation, Nucleic acid sequence analysis Nucleic acid sites, features and motifs Nucleic acid sites, features and motifs peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh blast_rbh blast_rbh This tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 336 411 18624 27781 0 0 0 0 0 0 0 0 0 0 0 0 336 1083 18624 65029 https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a
blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs 2016-01-05 http://artbio.fr 1.1.0 python To update RNA, Sequence Analysis, Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 8 8 0 0 0 0 0 0 0 0 1 3 8 24
blast_unmatched blast_unmatched Extract unmatched query sequences from blast 2017-10-03 http://artbio.fr 1.0.1 python To update Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits 2017-10-15 http://artbio.fr 2.7.1 python To update Assembly, RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 8 8 0 0 0 0 0 0 0 0 1 3 8 24
blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs 2015-06-17 http://artbio.fr 1.1.1 python To update RNA, Sequence Analysis, Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions 2013-09-23 https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python To update Convert Formats, Sequence Analysis, Text Manipulation Sequence alignment, Sequence annotation Sequence alignment, Sequence annotation Sequence analysis Sequence analysis peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr blastxml_to_top_descr blastxml_to_top_descr This tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 521 617 263808 265716 0 0 0 0 0 0 0 0 0 0 0 0 521 1659 263808 793332 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4
bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch 2015-08-28 http://proteowizard.sourceforge.net/ 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 23 36 980 1439 0 0 0 0 0 0 0 0 0 0 0 0 23 82 980 3399
c3s c3s Copernicus Climate Change Service (C3S) 2021-04-13 https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset 0.3.0 python To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 15 15 340 340 5 5 6 6 3 3 113 113 0 0 0 0 23 69 459 1377 https://dev.workflowhub.eu/workflows/1312?version=1, https://usegalaxy.eu/published/workflow?id=21363a774a7575f0, https://usegalaxy.eu/published/workflow?id=ac5b66c42681e7a8, https://usegalaxy.eu/published/workflow?id=b610849d70c1e225, https://usegalaxy.eu/published/workflow?id=ddb21f7793eff83d climate/earth_system, contributing/create-new-tutorial
cads cads Copernicus Atmosphere Data Store (ADS) 2021-06-19 https://ads.atmosphere.copernicus.eu/#!/home 0.1.0 python To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 52 52 0 0 0 0 0 0 0 0 0 0 0 0 1 3 52 156
calisp calisp Calgary approach to isotopes in proteomics 2023-06-01 https://github.com/kinestetika/Calisp/ 3.0.13 calisp 3.1.4 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 223 223 0 0 0 0 0 0 0 0 0 0 0 0 3 9 223 669
cap3 cap3 cap3 wrapper 2017-09-02 http://artbio.fr 2.0.1 cap3 10.2011 To update Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 208 208 11740 11740 0 0 0 0 158 158 7360 7360 0 0 0 0 366 1098 19100 57300 https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33
cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets 2018-10-01 http://cardinalmsi.org 3.4.3 bioconductor-cardinal 3.8.0 To update Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 0 9 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 11 9 0 675 743 38090 50857 1 1 12 12 231 231 8501 8501 101 101 129 129 1008 3092 46732 152963 https://dev.workflowhub.eu/workflows/1061?version=1, https://dev.workflowhub.eu/workflows/1123?version=1, https://dev.workflowhub.eu/workflows/1184?version=1, https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=785433e42d82be65, https://usegalaxy.eu/published/workflow?id=7ee6976f69131683, https://usegalaxy.eu/published/workflow?id=9e497c5c9e64d9b3, https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73, https://usegalaxy.eu/published/workflow?id=f4a55ef0d4c2cd97, https://usegalaxy.eu/published/workflow?id=fb233e418d015649, https://usegalaxy.org.au/published/workflow?id=04f6ad62f34313ea, https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89, https://usegalaxy.org.au/published/workflow?id=80cf8be8c8bf384a metabolomics/msi-analyte-distribution, metabolomics/msi-finding-nglycans, proteomics/mass-spectrometry-imaging-loading-exploring-data
cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. 2021-09-01 https://code.mpimet.mpg.de/projects/cdo/ 2.0.0 To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 18 18 228 228 0 0 0 0 0 0 0 0 0 0 0 0 18 54 228 684 https://dev.workflowhub.eu/workflows/1260?version=1, https://usegalaxy.eu/published/workflow?id=4f0f3b911b4e4921, https://usegalaxy.eu/published/workflow?id=6afc245029ce5008, https://usegalaxy.eu/published/workflow?id=b4bfcbf8acee9cc3, https://usegalaxy.eu/published/workflow?id=d94460f342b70eb3 ecology/x-array-map-plot
cds_essential_variability cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability 2019-05-03 https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview 0.2.0 python To update Climate Analysis, Data Source climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 38 40 191 336 0 0 0 0 0 0 0 0 0 0 0 0 38 116 191 718 https://dev.workflowhub.eu/workflows/1138?version=2, https://usegalaxy.eu/published/workflow?id=392a5d91ac221104, https://usegalaxy.eu/published/workflow?id=f774cf05ddff3612 climate/climate-101
cesm cesm Community Earth System Model (CESM) 2021-06-15 https://www.cesm.ucar.edu/ 2.1.3 cesm 2.1.3 Up-to-date Climate Analysis climate https://github.com/ESCOMP/CESM https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 14 14 0 0 0 0 0 0 0 0 0 0 0 0 2 6 14 42 https://usegalaxy.eu/published/workflow?id=46b4ad3ce0b7bc0b
champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields 2022-10-28 0.0.0 r-base To update Ecology ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 21 21 205 205 0 0 0 0 0 0 0 0 4 4 11 11 25 75 216 648 https://dev.workflowhub.eu/workflows/1256?version=1, https://usegalaxy.eu/published/workflow?id=a3ad27817f77061b, https://workflowhub.eu/workflows/661?version=1 ecology/champs-blocs
checkv checkv_end_to_end Assess quality of single-contig viral genomes 2024-09-13 https://bitbucket.org/berkeleylab/checkv/ 1.0.3 checkv 1.0.3 Up-to-date Metagenomics Sequence assembly, Validation, Read mapping Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 38 38 0 0 0 0 0 0 0 0 0 0 0 0 9 27 38 114
cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content 2015-06-17 http://artbio.fr 4.1 python To update Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
climate_stripes climate_stripes Create climate stripes from a tabular input file 2019-10-05 https://www.climate-lab-book.ac.uk/2018/warming-stripes/ 1.0.2 python To update Climate Analysis, Visualization climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 35 218 239 3 3 19 19 3 3 224 224 0 0 0 0 40 121 461 1404 https://dev.workflowhub.eu/workflows/1138?version=2, https://dev.workflowhub.eu/workflows/1195?version=2, https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=392a5d91ac221104, https://workflowhub.eu/workflows/123?version=1 climate/climate-101, climate/pangeo
concatenate_multiple_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. 2018-03-11 http://artbio.fr 1.4.3 To update Text Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 752 753 9303 9305 319 319 2156 2156 242 297 2917 3974 1 1 3 3 1314 3998 14379 44196 https://usegalaxy.eu/published/workflow?id=03ef267ff7634a4b, https://usegalaxy.eu/published/workflow?id=18af9bbae833f8fe, https://usegalaxy.eu/published/workflow?id=373d861ef4b0081a, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=6aaf2b342d57f78d, https://usegalaxy.eu/published/workflow?id=7bda7ae31c427347, https://usegalaxy.eu/published/workflow?id=7cbda24fd0767899, https://usegalaxy.eu/published/workflow?id=82879b0eb4a71ad0, https://usegalaxy.eu/published/workflow?id=841367f185aaade4, https://usegalaxy.eu/published/workflow?id=8c6371b360217f72, https://usegalaxy.eu/published/workflow?id=b0377f05f97b18b1, https://usegalaxy.eu/published/workflow?id=b6457cb04bf31613, https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://usegalaxy.eu/published/workflow?id=e8a8c0b59ba9d593, https://usegalaxy.eu/published/workflow?id=ea3b120f105434ec, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org/published/workflow?id=2a4823c060dd216e, https://usegalaxy.org/published/workflow?id=31186e478383465b, https://usegalaxy.org/published/workflow?id=3511da8b41b1fb5d, https://usegalaxy.org/published/workflow?id=412da1489d6aed45, https://usegalaxy.org/published/workflow?id=46207bf9ce5ee26a, https://usegalaxy.org/published/workflow?id=4680511d4daad5d7, https://usegalaxy.org/published/workflow?id=4c996921fb6a2334, https://usegalaxy.org/published/workflow?id=696b2efc589afd6f, https://usegalaxy.org/published/workflow?id=7454015793c4adc9, https://usegalaxy.org/published/workflow?id=8b4945a0fb49e03e, https://usegalaxy.org/published/workflow?id=a97c694b3298ae44, https://usegalaxy.org/published/workflow?id=ac3755c1ae5f7f16, https://usegalaxy.org/published/workflow?id=af85a2ae187409f4, https://usegalaxy.org/published/workflow?id=b7c67632a6eabda5, https://usegalaxy.org/published/workflow?id=c7693951c6215e19, https://usegalaxy.org/published/workflow?id=d1ca40dd7e591025, https://usegalaxy.org/published/workflow?id=d485bf21a5069fe4, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/233?version=1, https://workflowhub.eu/workflows/622?version=11 proteomics/proteogenomics-dbcreation
consalign aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences 2023-04-11 1.0.0 r-bioseq To update Sequence Analysis ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 198 198 1511 1511 0 0 0 0 0 0 0 0 14 14 4349 4349 212 636 5860 17580 https://dev.workflowhub.eu/workflows/1287?version=2, https://dev.workflowhub.eu/workflows/1292?version=2, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a sequence-analysis/Manage_AB1_Sanger
consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment 2015-11-05 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab 2017-07-27 https://github.com/open2c/cooler 0.9.3 htslib 1.22 To update Epigenetics lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 4 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 44 44 298 298 56 56 236 236 0 0 0 0 0 0 0 0 100 300 534 1602 https://usegalaxy.eu/published/workflow?id=1214523f54a999fc, https://usegalaxy.eu/published/workflow?id=2a9c812f59b7b36c, https://usegalaxy.eu/published/workflow?id=4464d3b0fc782a1a, https://usegalaxy.eu/published/workflow?id=506a451679fe25b4, https://usegalaxy.eu/published/workflow?id=72201ffaf488f278, https://usegalaxy.eu/published/workflow?id=9843ae66c3b367b7, https://usegalaxy.eu/published/workflow?id=9f8a93cfffb31cd6, https://usegalaxy.eu/published/workflow?id=9fc8b89954c04ee1, https://usegalaxy.eu/published/workflow?id=ceb0a029c6d33ec6, https://usegalaxy.eu/published/workflow?id=d9fc0df2a159e542, https://usegalaxy.eu/published/workflow?id=f394d1b12779ba41, https://usegalaxy.eu/published/workflow?id=fc4e3479d86f9a26, https://usegalaxy.org/published/workflow?id=06eaa5b141fe7a08, https://usegalaxy.org/published/workflow?id=0bc1b8888d8b20c4, https://usegalaxy.org/published/workflow?id=1dc312e3fba9f810, https://usegalaxy.org/published/workflow?id=1e4eb6ccb47d9fc7, https://usegalaxy.org/published/workflow?id=4998f171ec922c7d, https://usegalaxy.org/published/workflow?id=7353afb9301780e5, https://usegalaxy.org/published/workflow?id=a93eb877596ce0ef, https://usegalaxy.org/published/workflow?id=b31ab9e76409a9b7, https://usegalaxy.org/published/workflow?id=c8a92318855d85a5, https://usegalaxy.org/published/workflow?id=f13432eef7ac28e9, https://usegalaxy.org/published/workflow?id=f21d576695f9fe77, https://usegalaxy.org/published/workflow?id=f80b80aa7fb196ba, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/420?version=3
cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts 2018-07-11 http://artbio.fr 0.6.0 r-optparse 1.3.2 To update Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
crbeam_astro_tool crbeam_astro_tool CRbeam 2024-01-31 0.0.2+galaxy0 crbeam To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/crbeam 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cta_astro_tool cta_astro_tool Basic simulation of CTA telescope observations using gammapy package 2024-04-19 0.0.1+galaxy0 unzip To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 3
ctsm_fates ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model 2020-10-21 https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api 2.0 fates-emerald To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 70 70 268 268 11 11 34 34 1 1 124 124 0 0 0 0 82 246 426 1278 https://dev.workflowhub.eu/workflows/1185?version=2, https://usegalaxy.eu/published/workflow?id=7b50e72deb46c6e8 climate/fates
custom_pro_db custom_pro_db CustomProDB 2017-10-06 https://bioconductor.org/packages/release/bioc/html/customProDB.html 1.22.0 bioconductor-rgalaxy 1.37.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 146 151 1723 1775 77 77 461 461 13 13 425 425 0 0 0 0 236 713 2609 7879 https://dev.workflowhub.eu/workflows/1042?version=1, https://dev.workflowhub.eu/workflows/1201?version=2, https://dev.workflowhub.eu/workflows/1386?version=1, https://dev.workflowhub.eu/workflows/1398?version=1, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.eu/published/workflow?id=c3f2350f0be2d9c9, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474 proteomics/neoantigen-2-non-reference-database-generation, proteomics/proteogenomics-dbcreation
custom_pro_db_annotation_data_manager CustomProDB Annotation 2017-10-06 https://bioconductor.org/packages/release/bioc/html/customProDB.html To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools 2021-06-23 0.0.0 r-tangles To update Ecology ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 458 458 1212 1212 0 0 0 0 0 0 0 0 17 17 40 40 475 1425 1252 3756 https://dev.workflowhub.eu/workflows/1278?version=1, https://usegalaxy.eu/published/workflow?id=7b576a562031ff7e, https://usegalaxy.eu/published/workflow?id=a0404f6291874c01, https://workflowhub.eu/workflows/656?version=1 ecology/biodiversity-data-exploration
data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper 2019-11-11 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper 2019-11-11 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dbbuilder dbbuilder Protein Database Downloader 2015-01-24 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 918 1053 6311 7176 10 10 26 26 94 94 1135 1135 13 13 26 26 1035 3240 7498 23359 https://dev.workflowhub.eu/workflows/1199?version=2, https://dev.workflowhub.eu/workflows/1204?version=2, https://dev.workflowhub.eu/workflows/1351?version=1, https://dev.workflowhub.eu/workflows/1354?version=1, https://dev.workflowhub.eu/workflows/1369?version=1, https://dev.workflowhub.eu/workflows/1372?version=1, https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=5374daf356516a40, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=73dc2384535bf6af, https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=cb9a26ea53ce7a27, https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2, https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=eeb6cff210cac091, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.org.au/published/workflow?id=65a659982f955743, https://usegalaxy.org.au/published/workflow?id=7cddb345877f08bf, https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1225?version=1 microbiome/clinical-mp-1-database-generation, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/database-handling
decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. 2015-01-24 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
deseq2_normalization deseq2_normalization Normalizes gene hitlists 2018-01-05 http://artbio.fr 1.40.2+galaxy1 bioconductor-deseq2 1.46.0 To update Transcriptomics, Statistics, Single Cell artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
desi_legacy_survey_astro_tool desi_legacy_survey_astro_tool Tool to query Legacy Survey data 2024-11-14 0.0.1+galaxy0 astropy To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/desi-legacy-survey 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dfast dfast Prokaryotic genome annotation 2025-04-16 https://github.com/nigyta/dfast_core/ 1.3.6 dfast 1.3.6 Up-to-date Genome annotation Genome annotation Genome annotation Nucleic acid structure analysis, Genomics, Sequence analysis Nucleic acid structure analysis, Genomics, Sequence analysis ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/dfast/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/dfast dfast DFAST Flexible prokaryotic genome annotation pipeline for faster genome publication. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dfpl dfpl_predict, dfpl_train Galaxy wrapper for deepFPlearn. 2024-12-18 https://github.com/yigbt/deepFPlearn 2.1 deepfplearn 2.1 Up-to-date Computational chemistry, Machine Learning ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/dfpl https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/dfpl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dia_umpire dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics 2015-08-26 http://diaumpire.sourceforge.net/ 2.1.3 dia_umpire 2.1.6 To update Proteomics galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 4 21 33 0 0 0 0 4 4 155 155 0 0 0 0 8 24 176 540
dialignr dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. 2020-12-23 https://github.com/shubham1637/DIAlignR 1.2.0 bioconductor-dialignr 2.10.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 40 40 0 0 0 0 0 0 0 0 0 0 0 0 2 6 40 120
diann diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. 2023-06-26 https://github.com/vdemichev/DiaNN 1.8.1 To update Proteomics galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 111 111 0 0 0 0 18 18 240 240 0 0 0 0 36 108 351 1053
diapysef diapysef diapysef is a convenience package for working with DIA-PASEF data 2020-02-27 https://pypi.org/project/diapysef/ 0.3.5.0 diapysef 1.0.10 To update Proteomics galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 40 40 266 266 0 0 0 0 6 6 319 319 0 0 0 0 46 138 585 1755 https://dev.workflowhub.eu/workflows/1039?version=1, https://dev.workflowhub.eu/workflows/1224?version=2 proteomics/DIA_lib_OSW
diffacto diffacto Diffacto comparative protein abundance estimation 2021-06-20 https://github.com/statisticalbiotechnology/diffacto 1.0.6 diffacto 1.0.7 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 11 11 0 0 0 0 0 0 0 0 0 0 0 0 7 21 11 33
digestdb digestdb 2015-01-24 0.1.0 trans_proteomic_pipeline To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
directag_and_tagrecon 2015-01-24 To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dose_response_analysis_tool dr_curve A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses 2024-04-06 https://github.com/bernt-matthias/mb-galaxy-tools 3.0.1 r-drc 3.0_1 To update Ecology ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
droplet_barcode_plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC 2019-11-07 https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary 1.6.1+galaxy2 scxa-plots 0.0.1 To update Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 234 234 1360 1364 81 81 365 365 1 1 23 23 0 0 0 0 316 948 1748 5248 https://dev.workflowhub.eu/workflows/1024?version=1, https://dev.workflowhub.eu/workflows/1025?version=1, https://dev.workflowhub.eu/workflows/1263?version=1, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=9ed36a6849fa2014, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d single-cell/scrna-case_alevin
earth landcover_subindicator Access, process, visualise oceanographic data for the Earth System 2024-10-21 https://github.com/Marie59/FE-ft-ESG/tree/main/earth 0.1.0 numpy To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 6
ecoregionalization ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ClaraGuess, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. 2023-07-26 https://github.com/PaulineSGN/Workflow_Galaxy 0.1.2+galaxy0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0 0 7 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 55 55 642 642 0 0 0 0 0 0 0 0 0 0 0 0 55 165 642 1926 https://dev.workflowhub.eu/workflows/1363?version=1, https://usegalaxy.eu/published/workflow?id=89ff2a1143954d83, https://workflowhub.eu/workflows/1208?version=1, https://workflowhub.eu/workflows/1209?version=1, https://workflowhub.eu/workflows/658?version=1 ecology/Ecoregionalization_tutorial, ecology/ecoregiolifetraits
eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences 2019-11-11 2.1.8 eggnog-mapper 2.1.12 To update Proteomics Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 3 3 0 1450 1456 39884 40140 134 134 985 985 498 498 22184 22184 149 149 65332 65332 2231 6699 128385 385411 https://dev.workflowhub.eu/workflows/1183?version=1, https://dev.workflowhub.eu/workflows/1202?version=1, https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4, https://workflowhub.eu/workflows/1262?version=1, https://workflowhub.eu/workflows/754?version=1, https://workflowhub.eu/workflows/755?version=1 genome-annotation/funannotate, genome-annotation/functional
embl2fa embl2fa Converts EMBL flat format to fasta format 2022-11-12 http://artbio.fr 0.2 To update Text Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
emlassemblyline annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa 2023-07-21 https://github.com/EDIorg/EMLassemblyline 0.1.0+galaxy0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0 0 11 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 148 148 618 618 0 0 0 0 0 0 0 0 0 0 0 0 148 444 618 1854 https://usegalaxy.eu/published/workflow?id=a30d511e3dda0895, https://usegalaxy.eu/published/workflow?id=ab89c61db3d7abbb
encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis 2020-09-11 https://bitbucket.org/searleb/encyclopedia/wiki/Home 1.12.34 encyclopedia 2.12.30 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 2 4 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 105 105 774 774 5 5 36 36 8 8 47 47 0 0 0 0 118 354 857 2571 https://dev.workflowhub.eu/workflows/1027?version=1, https://dev.workflowhub.eu/workflows/1146?version=3, https://usegalaxy.eu/published/workflow?id=14f9c2099db30570, https://usegalaxy.eu/published/workflow?id=3676aafc35dc2fe7, https://usegalaxy.eu/published/workflow?id=5d4e4b9f07a1ec20, https://usegalaxy.eu/published/workflow?id=5dec0e5a2d75cdc1, https://usegalaxy.eu/published/workflow?id=87c21b682af78ec9, https://usegalaxy.eu/published/workflow?id=9ac15b644c805a2b, https://usegalaxy.eu/published/workflow?id=f1309010689eb98a proteomics/encyclopedia
eodie eodie Earth Observation Data Information Extractor 2021-12-30 https://eodie.readthedocs.io/ 1.0.2 eodie To update Climate Analysis climate https://gitlab.com/eetun-tiimi/EODIE https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 45 45 0 0 0 0 0 0 0 0 0 0 0 0 4 12 45 135
ez_histograms ez_histograms ggplot2 histograms and density plots 2024-02-07 https://github.com/tidyverse/ggplot2 3.4.4 r-ggplot2 2.2.1 To update Visualization, Statistics Data analysis, Statistical calculation, Visualisation Statistical calculation, Visualisation Ecology Ecology artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms ez_histograms ez_histograms This tool produces histograms or density plots from any tabular datasets, using ggplot2.You may provide headerless tables as well as tables with column headers. Any non-numeric columns will be filtered out. Your first column may contains row names, but it will also work if your first column already corresponds to the numeric values of a variable. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together 2015-01-24 https://github.com/galaxyproteomics/tools-galaxyp/ 1.2.0 python To update Fasta Manipulation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 1274 1424 32878 34429 1505 1505 38138 38138 266 266 5572 5572 26 26 282 282 3071 9363 76870 232161 https://dev.workflowhub.eu/workflows/1042?version=1, https://dev.workflowhub.eu/workflows/1077?version=2, https://dev.workflowhub.eu/workflows/1199?version=2, https://dev.workflowhub.eu/workflows/1201?version=2, https://dev.workflowhub.eu/workflows/1204?version=2, https://dev.workflowhub.eu/workflows/1350?version=1, 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https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=2be8ecd5922d23d1, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=93810012f2610de4, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/102?version=1, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1216?version=1, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1225?version=1 microbiome/clinical-mp-1-database-generation, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/database-handling, proteomics/neoantigen-2-non-reference-database-generation, proteomics/neoantigen-3-fragpipe-discovery, proteomics/proteogenomics-dbcreation
fastg2protlib fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG 2020-07-23 https://github.com/galaxyproteomics/fastg2protlib.git 1.0.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 8 8 29 29 0 0 0 0 0 0 0 0 0 0 0 0 8 24 29 87
fastq_pair fastq_pair Paired-end fastq pairer 2022-03-17 https://github.com/linsalrob/fastq-pair 1.0+galaxy0 fastq-pair 1.0 To update Fastq Manipulation ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_quality_trimmer cshl_fastq_quality_trimmer FASTQ trimmer based on quality 2022-03-11 https://github.com/agordon/fastx_toolkit 0.0.14+galaxy0 fastx_toolkit 0.0.14 To update Fastq Manipulation ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files 2022-02-15 https://github.com/nunofonseca/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 To update Transcriptomics, RNA ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
feature_alignment feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy 2015-02-06 0.11.0 msproteomicstools 0.11.0 Up-to-date Proteomics galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 18 18 0 0 0 0 0 0 0 0 0 0 0 0 1 3 18 54
fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers 2015-06-17 http://artbio.fr 3.1.0 urllib3 1.12 To update Fasta Manipulation, Data Source artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 1 0 4 1 4 1 7
filter_by_fasta_ids filter_by_fasta_ids Filter FASTA on the headers and/or the sequences 2015-01-24 2.3 python To update Fasta Manipulation, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 1093 1175 104341 108230 1345 1345 50058 50058 259 259 10567 10567 47 47 446 446 2744 8314 165412 500125 https://dev.workflowhub.eu/workflows/1287?version=2, https://dev.workflowhub.eu/workflows/1292?version=2, https://dev.workflowhub.eu/workflows/1318?version=2, https://usegalaxy.eu/published/workflow?id=02f240f6cf72080a, https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5, https://usegalaxy.eu/published/workflow?id=1b38e0d69e366be1, https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09, https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50, https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a, https://usegalaxy.eu/published/workflow?id=82a60d94d699efbf, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab, https://usegalaxy.eu/published/workflow?id=b51559006f86db9e, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=fba0eb562a710733, https://usegalaxy.org/published/workflow?id=386d3b300cf05305, https://usegalaxy.org/published/workflow?id=3c7349268d74c576, https://usegalaxy.org/published/workflow?id=4884918895db9af0, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf, https://usegalaxy.org/published/workflow?id=89d3c800d3be6050, https://usegalaxy.org/published/workflow?id=94da3d448bb8a137, https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1 sequence-analysis/Manage_AB1_Sanger, sequence-analysis/tapscan-streptophyte-algae, transcriptomics/mirna-target-finder
filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. 2021-01-06 https://github.com/RECETOX/galaxytools/ 3.1.1 openbabel 2.3.90dev7d621d9 To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_density filterdensity Filter out position based on distance between SNVs 2015-11-19 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_stats filterstat SNVPhyl filter_stats 2015-07-31 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_vcf filtervcf SNVPhyl filter_vcf 2015-08-04 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer 2015-07-31 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fishertest fishertest Fisher's exact test on two-column hit lists. 2015-06-17 http://artbio.fr 2.32.0+galaxy0 bioconductor-qvalue 2.38.0 To update RNA, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
flashlfq flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification 2017-12-06 https://github.com/smith-chem-wisc/FlashLFQ 1.0.3.1 flashlfq 2.0.0 To update Proteomics Label-free quantification Label-free quantification Proteomics experiment, Proteomics Proteomics experiment, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 54 57 630 722 0 0 0 0 15 15 189 189 0 0 0 0 69 210 819 2549 https://dev.workflowhub.eu/workflows/1177?version=2, https://dev.workflowhub.eu/workflows/1338?version=1, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d proteomics/metaquantome-data-creation
fragpipe fragpipe Data analysis for mass spectrometry-based proteomics. 2022-07-21 https://fragpipe.nesvilab.org/ 20.0 fragpipe 23.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 177 177 11 11 33 33 0 0 0 0 0 0 0 0 32 96 210 630 https://dev.workflowhub.eu/workflows/1384?version=1, https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85, https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e proteomics/neoantigen-3-fragpipe-discovery
freeenergy Free energy tools of BRIDGE. 2019-10-24 To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis 2021-08-16 http://frogs.toulouse.inrae.fr/ 4.2.0 frogs 5.0.2 To update Metagenomics frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 0 0 0 28 0 0 0 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9415 9417 60651 60685 9415 28247 60651 181987 https://usegalaxy.fr/published/workflow?id=048cb90ec1ac7120, https://usegalaxy.fr/published/workflow?id=2ac84b2bd45876cf, https://usegalaxy.fr/published/workflow?id=b46954345641a3b8, https://usegalaxy.fr/published/workflow?id=d68b4aa5337f016b
from_hicup_to_juicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. 2018-06-05 0.0.2 pysam 0.23.2 To update Epigenetics lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fromgtftobed12 fromgtfTobed12 Convert GTF files to BED12 format 2019-07-31 https://pythonhosted.org/gffutils/contents.html 0.11.1+galaxy1 gffutils 0.13 To update Convert Formats lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations 2021-12-29 http://artbio.fr 4.1.7.0 gatk4 4.6.2.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gc_derivatization gc_derivatization In silico derivatization for GC. 2024-03-15 https://github.com/RECETOX/gc-meox-tms 1.0.1 gc-meox-tms 1.0.1 Up-to-date Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 3 3 0 0 0 0 1 1 19 19 0 0 0 0 2 6 22 66
gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. 2019-02-25 https://www.gdal.org 3.0.0 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 40 43 1222 1508 0 0 0 0 0 0 0 0 2 2 3 3 42 129 1225 3961 https://dev.workflowhub.eu/workflows/1268?version=2, https://usegalaxy.eu/published/workflow?id=3b0803542deff026, https://usegalaxy.eu/published/workflow?id=b0b6c8756070650b, https://workflowhub.eu/workflows/404?version=1 ecology/gbif_cleaning
genomad genomad_end_to_end Identify virus and plasmid genomes from nucleotide sequences 2024-06-17 https://github.com/apcamargo/genomad/ 1.8.0 genomad 1.11.0 To update Metagenomics Sequence annotation, Taxonomic classification Sequence annotation, Taxonomic classification Sequence analysis Sequence analysis ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad genomad geNomad geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 1658 1658 0 0 0 0 0 0 0 0 0 0 0 0 42 126 1658 4974
get_reference_fasta get_fasta_reference Obtain reference genome sequence. 2015-06-17 http://artbio.fr 0.3.2 To update Data Source, Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gettn5extendedcoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension 2018-06-13 0.0.2 pysam 0.23.2 To update Epigenetics lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gffcompare_to_bed gffcompare_to_bed Filter and convert a gffCompare GTF to BED 2018-01-10 https://github.com/gpertea/gffcompare/ 0.2.1 python To update Convert Formats galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 337 365 1314 2282 406 406 1153 1153 71 71 566 566 0 0 0 0 814 2470 3033 10067 https://dev.workflowhub.eu/workflows/1042?version=1, https://dev.workflowhub.eu/workflows/1201?version=2, https://dev.workflowhub.eu/workflows/1386?version=1, https://dev.workflowhub.eu/workflows/1398?version=1, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474 proteomics/neoantigen-2-non-reference-database-generation, proteomics/proteogenomics-dbcreation
gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. 2018-10-03 https://github.com/gromacs 2022 gromacs 2021.3 To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 14 8 15 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 15 9 0 3897 3963 186315 191332 1763 1763 11409 11409 782 782 12212 12212 0 0 0 0 6442 19392 209936 634825 https://dev.workflowhub.eu/workflows/1062?version=1, https://dev.workflowhub.eu/workflows/1130?version=2, https://dev.workflowhub.eu/workflows/1134?version=1, https://usegalaxy.eu/published/workflow?id=07e1478df88a17cc, https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=1b10ece62e745125, https://usegalaxy.eu/published/workflow?id=2a1b21d39ebb6e49, https://usegalaxy.eu/published/workflow?id=3729015f676693c8, https://usegalaxy.eu/published/workflow?id=3c6ff60d1d3ceb3d, https://usegalaxy.eu/published/workflow?id=5d793801998146bc, https://usegalaxy.eu/published/workflow?id=7969bdac8adb8810, https://usegalaxy.eu/published/workflow?id=843c10c447496280, https://usegalaxy.eu/published/workflow?id=84c95f31896213fd, https://usegalaxy.eu/published/workflow?id=abd1cb3457338eb5, https://usegalaxy.eu/published/workflow?id=ac84daeb82d76e1c, https://usegalaxy.eu/published/workflow?id=adc6d049e9283789, https://usegalaxy.eu/published/workflow?id=b51b2f4950d26b07, https://usegalaxy.eu/published/workflow?id=bf99d06567288766, https://usegalaxy.eu/published/workflow?id=c39a79bb45b2566e, https://usegalaxy.eu/published/workflow?id=d1357759d0962144, https://usegalaxy.eu/published/workflow?id=d4d8e907e26c8587, https://usegalaxy.eu/published/workflow?id=d873ff816f028d4f, https://usegalaxy.eu/published/workflow?id=d91e715b5e3457d3, https://usegalaxy.eu/published/workflow?id=e0dddc2579c3614e, https://usegalaxy.eu/published/workflow?id=e3b0b521ee8f2aef, https://usegalaxy.eu/published/workflow?id=e73beff62f35d677, https://usegalaxy.eu/published/workflow?id=fb425d6accf3ca55, https://usegalaxy.org.au/published/workflow?id=28cf646b95e4d3ab, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0, https://usegalaxy.org.au/published/workflow?id=8a20b3ed4a81263d, https://usegalaxy.org/published/workflow?id=00a4dbc9329c638b, https://usegalaxy.org/published/workflow?id=0fb89e9c397c8938, https://usegalaxy.org/published/workflow?id=183254b3565bcb04, https://usegalaxy.org/published/workflow?id=195a608c481040de, https://usegalaxy.org/published/workflow?id=28c7e8269d478244, https://usegalaxy.org/published/workflow?id=3c1e2bbb1a77cc30, https://usegalaxy.org/published/workflow?id=442a2868873e7f77, https://usegalaxy.org/published/workflow?id=634bbef1f67a0e30, https://usegalaxy.org/published/workflow?id=a638e12411586555, https://usegalaxy.org/published/workflow?id=aaec757e04605d3a, https://usegalaxy.org/published/workflow?id=ad19db6504b6dc33, https://usegalaxy.org/published/workflow?id=d2b994833b79d2cb, https://workflowhub.eu/workflows/247?version=2, https://workflowhub.eu/workflows/248?version=4, https://workflowhub.eu/workflows/249?version=2, https://workflowhub.eu/workflows/761?version=1, https://workflowhub.eu/workflows/762?version=1, https://workflowhub.eu/workflows/763?version=1, https://workflowhub.eu/workflows/764?version=1 computational-chemistry/htmd-analysis, computational-chemistry/md-simulation-gromacs
gsc_center_scale center_scale Center or scale (standardize) data 2019-07-09 http://artbio.fr 4.3.1+galaxy1 r-optparse 1.3.2 To update Statistics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_filter_cells filter_cells Filter single cell RNAseq data on library depth and number of detected genes 2019-06-23 http://artbio.fr 4.3.1+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data 2019-06-23 http://artbio.fr 4.3.1+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations 2019-06-24 http://artbio.fr 4.3.1+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation 2019-06-23 http://artbio.fr 4.3+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Visualization, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data 2019-06-23 http://artbio.fr 4.1.3+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_scran_normalize scran_normalize Normalize raw counts using scran 2019-09-23 http://artbio.fr 1.28.1+galaxy1 bioconductor-scran 1.34.0 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 27 27 106 106 13 13 322 322 4 4 80 80 0 0 0 0 44 132 508 1524
gsc_signature_score signature_score Compute signature scores from single cell RNAseq data 2019-06-23 http://artbio.fr 2.3.9+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gtf2gene_list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. 2019-11-07 https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 To update Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 401 405 2304 2321 391 391 1173 1173 42 42 240 240 0 0 0 0 834 2506 3717 11168 https://dev.workflowhub.eu/workflows/1024?version=1, https://dev.workflowhub.eu/workflows/1025?version=1, https://dev.workflowhub.eu/workflows/1263?version=1, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=50f8693fac7e134b, https://usegalaxy.eu/published/workflow?id=73b41b975da284d5, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=9ed36a6849fa2014, https://usegalaxy.eu/published/workflow?id=aeb0f5b74e51f5c2, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=e97bdba3834ac465, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d single-cell/scrna-case_alevin
guppy_basecaller guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies 2020-11-18 http://artbio.fr 6.5.7+galaxy0 To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 7 7 0 0 0 0 1 3 7 21
hardklor hardklor, kronik Hardklör 2016-04-26 2.30.1+galaxy1 hardklor 2.3.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 5 8 78 111 0 0 0 0 0 0 0 0 0 0 0 0 5 18 78 267
hess_astro_tool hess_astro_tool Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope 2024-02-19 0.0.2+galaxy0 ipython To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 6 https://workflowhub.eu/workflows/766?version=1
high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps 2019-07-20 https://github.com/cran/gplots 3.1.3+galaxy0 r-gplots 2.17.0 To update Visualization artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hirieftools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools 2017-04-11 1.3 python To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hirondelle_crim_ogc_api_processes hirondelle_crim This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. 2024-06-07 https://github.com/AquaINFRA/galaxy 0.2.0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 236 236 0 0 0 0 0 0 0 0 0 0 0 0 3 9 236 708 https://usegalaxy.eu/published/workflow?id=6173008772bdba09, https://usegalaxy.eu/published/workflow?id=b1fa4a3561988704
hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack 2023-02-27 20241220 Fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
idconvert idconvert Convert mass spectrometry identification files on linux or MacOSX 2019-02-22 proteowizard 3_0_9992 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 21 33 197 277 0 0 0 0 0 0 0 0 0 0 0 0 21 75 197 671
incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server 2023-02-17 20231221 Fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file 2024-01-05 https://github.com/AquaINFRA/galaxy 1.0 r-getopt To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 70 70 0 0 0 0 0 0 0 0 0 0 0 0 7 21 70 210 https://usegalaxy.eu/published/workflow?id=0b2304aa2083bd1a, https://workflowhub.eu/workflows/807?version=1
ipaPy2 ipapy2_MS1_annotation, ipapy2_MS2_annotation, ipapy2_clustering, ipapy2_compute_all_adducts, ipapy2_compute_bio, ipapy2_gibbs_sampler, ipapy2_gibbs_sampler_add, ipapy2_map_isotope_patterns Mass spectrometry data annotation tool. 2023-12-04 https://github.com/francescodc87/ipaPy2 1.3.0 ipapy2 1.3.0 Up-to-date Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
iphop iphop_predict Integrated Phage Host Prediction 2024-10-14 https://bitbucket.org/srouxjgi/iphop/ 1.3.3 iphop 1.3.3 Up-to-date Metagenomics Sample comparison Sample comparison ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop iphop iPHoP An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
isolib isolib Create an isotopic pattern library for given compounds and adducts. 2023-10-26 https://github.com/RECETOX/galaxytools/ 2.6+galaxy1 bioconductor-metabocoreutils 1.14.0 To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3 3 0 0 0 0 1 1 60 60 0 0 0 0 3 9 63 189
justdiff justdiff Unix diff 2017-09-27 http://artbio.fr 3.10+galaxy0 diffutils To update Text Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
justgzip justgzip Compress fastq sequence files 2018-05-16 http://artbio.fr 2.8+galaxy0 pigz To update Convert Formats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 20 20 1 3 20 60
lambdaminer lm_get_projects Lambda-Miner Tools 2025-03-06 https://lambda-miner-project.pages.ufz.de/lambda-miner-workflows/ 0.1.0+galaxy0 pandas To update Web Services, Data Source ufz https://github.com/jw44lavo/galaxy-tools/blob/bgo/tools/lambdaminer/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/lambdaminer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lfq_protein_quant lfq_protein_quant Enable protein summarisation and quantitation 2018-10-02 https://github.com/compomics/LFQ_galaxy_p 1.0 bioconductor-msnbase 2.32.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 12 19 70 116 0 0 0 0 0 0 0 0 0 0 0 0 12 43 70 256
longorf longORF obtain longest ORF in six-frame translations 2018-06-01 0.3.0 To update Sequence Analysis mbernt https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ltq_iquant_cli 2015-01-24 To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow 2020-07-12 http://artbio.fr 0.2.8+galaxy1 svtyper 0.7.1 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lumpy_sv lumpy Find structural variations 2017-07-24 http://artbio.fr 1.3 lumpy-sv 0.3.1 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
make_nr make_nr Make a FASTA file non-redundant 2018-11-06 https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 To update Fasta Manipulation, Sequence Analysis Sequence alignment, Genome annotation Sequence alignment, Genome annotation Molecular biology, Sequence analysis Molecular biology, Sequence analysis peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr make_nr make_nr Make a FASTA file non-redundant, with a Galaxy wrapperThis tool is copyright 2018 by Peter Cock, The James Hutton Institute, UK. All rights reserved.This tool is a short Python script intended to be run prior to calling the NCBI BLAST+ command line tool makeblastdb or in other settings where you want to collapse duplicated sequences in a FASTA file to a single representative. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
manta manta Structural variant and indel caller for mapped sequencing data 2019-10-25 http://artbio.fr 1.6 manta 1.6.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta https://github.com/ARTbio/tools-artbio/tree/main/tools/manta 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 53 53 568 568 0 0 0 0 0 0 0 0 0 0 0 0 53 159 568 1704
map_peptides_to_bed map_peptides_to_bed Map peptides to a reference genome for display by a genome browser 2016-01-13 0.2 biopython 1.70 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 8 9 33 46 0 0 0 0 0 0 0 0 0 0 0 0 8 25 33 112
mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file 2022-06-15 http://artbio.fr 0.22.0 r-optparse 1.3.2 To update Sequence Analysis, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
marine_omics sanntis_marine The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data 2024-07-26 https://github.com/Finn-Lab/SanntiS 0.9.3.5 sanntis 0.9.4.1 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 67 67 0 0 0 0 2 2 42 42 0 0 0 0 9 27 109 327 https://dev.workflowhub.eu/workflows/1357?version=1, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b ecology/marine_omics_bgc
matchms matchms_add_key, matchms_convert, matchms_matchms_export_skyline_transition_list, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. 2020-11-16 https://github.com/matchms/matchms 0.27.0 matchms 0.30.0 To update Metabolomics Spectral library search, Format validation, Filtering Spectral library search, Format validation, Filtering Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. 2 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 81 81 1699 1699 9 9 28 28 18 18 2754 2754 47 47 305 305 155 465 4786 14358 https://dev.workflowhub.eu/workflows/1119?version=2, https://usegalaxy.eu/published/workflow?id=3086366b744e8da9, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://workflowhub.eu/workflows/888?version=2 metabolomics/gc_ms_with_xcms
max_projections_stack_and_upload_omero max_projections_stack_and_upload_omero Combine images from max projections to stack and upload to the omero server 2024-12-12 20241213.2 Fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
maxquant maxquant, maxquant_mqpar wrapper for MaxQuant 2015-01-24 https://www.maxquant.org/ 2.0.3.0 maxquant 2.0.3.0 Up-to-date Proteomics Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability Proteomics experiment, Proteomics, Statistics and probability galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1600 1629 7822 8085 672 672 3257 3257 377 377 3472 3472 0 0 0 0 2649 7976 14551 43916 https://dev.workflowhub.eu/workflows/1026?version=1, https://dev.workflowhub.eu/workflows/1039?version=1, https://dev.workflowhub.eu/workflows/1140?version=2, https://dev.workflowhub.eu/workflows/1224?version=2, https://dev.workflowhub.eu/workflows/1227?version=2, https://dev.workflowhub.eu/workflows/1240?version=1, https://dev.workflowhub.eu/workflows/1353?version=1, https://dev.workflowhub.eu/workflows/1354?version=1, https://dev.workflowhub.eu/workflows/1368?version=1, https://dev.workflowhub.eu/workflows/1369?version=1, https://usegalaxy.eu/published/workflow?id=0135ee4b3fa0cbce, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=96d198ed953449fd, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=d789165f4e0c50eb, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://usegalaxy.org.au/published/workflow?id=43a951ec514498f6, https://usegalaxy.org.au/published/workflow?id=781457327e644c7e, https://usegalaxy.org.au/published/workflow?id=b0a79310e0dc3fb4, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=2404d5e5b1817825, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1177?version=1, https://workflowhub.eu/workflows/1225?version=1 microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-4-quantitation, proteomics/DIA_lib_OSW, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-4-quantitation, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq, proteomics/maxquant-msstats-tmt
md_converter md_converter A tool for interconverting between different MD structure and trajectory file formats. 2018-10-13 1.9.7 mdtraj To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 294 298 27209 27307 59 59 809 809 62 62 1129 1129 0 0 0 0 415 1249 29147 87539 https://dev.workflowhub.eu/workflows/1062?version=1, https://usegalaxy.eu/published/workflow?id=07e1478df88a17cc, https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=3c6ff60d1d3ceb3d, https://usegalaxy.eu/published/workflow?id=843c10c447496280, https://usegalaxy.eu/published/workflow?id=abd1cb3457338eb5, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0, https://usegalaxy.org/published/workflow?id=0fb89e9c397c8938, https://usegalaxy.org/published/workflow?id=183254b3565bcb04, https://usegalaxy.org/published/workflow?id=3c1e2bbb1a77cc30, https://usegalaxy.org/published/workflow?id=442a2868873e7f77, https://usegalaxy.org/published/workflow?id=ad19db6504b6dc33, https://workflowhub.eu/workflows/248?version=4 computational-chemistry/htmd-analysis, computational-chemistry/med-chem-data, fair/med-chem-data
md_converter md_slicer A tool for slicing trajectory files using MDTraj. 2019-10-07 1.9.9 mdtraj To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 19 20 157 177 4 4 6 6 7 7 483 483 0 0 0 0 30 91 646 1958
mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations 2018-10-04 https://github.com/MDAnalysis/mdanalysis 1.0.0 mdanalysis To update Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 10 5 10 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 342 362 3176 3390 61 61 197 197 44 44 614 614 0 0 0 0 447 1361 3987 12175 https://dev.workflowhub.eu/workflows/1062?version=1, https://dev.workflowhub.eu/workflows/1126?version=1, https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=b47e415f80941ba0, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0 computational-chemistry/analysis-md-simulations, computational-chemistry/htmd-analysis
mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories 2020-06-24 https://github.com/mdtraj/mdtraj 1.9.7 mdtraj To update Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 36 36 4 4 63 63 0 0 0 0 0 0 0 0 12 36 99 297
mean_per_zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file 2019-03-15 https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ 0.2.0 python To update Visualization, GIS, Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 3 12 25 0 0 0 0 0 0 0 0 0 0 0 0 2 7 12 49
measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index 2022-01-18 20221216 fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa 2023-11-30 https://github.com/jeremyfix/medenv 0.1.0 pandas To update Ecology, Data Source ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11 34 34 0 0 0 0 0 0 0 0 0 0 0 0 11 33 34 102
meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer 2017-03-03 https://github.com/compomics/meta-proteome-analyzer/ 2.0.0 mpa-portable 2.0.0 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 142 142 0 0 0 0 0 0 0 0 0 0 0 0 21 63 142 426
metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage 2018-03-21 http://metagene.nig.ac.jp/ 1.0 metagene_annotator 1.0 Up-to-date Sequence Analysis Sequence annotation Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Genomics, Model organisms, Data submission, annotation and curation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 379 379 1198 1198 0 0 0 0 0 0 0 0 0 0 0 0 379 1137 1198 3594 https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=799b924edd3c401b, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178
metanovo metanovo Produce targeted databases for mass spectrometry analysis. 2022-03-29 https://github.com/uct-cbio/proteomics-pipelines 1.9.4 metanovo 1.9.4 Up-to-date Proteomics Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 37 37 4908 4908 1 1 6 6 3 3 42 42 0 0 0 0 41 123 4956 14868 https://dev.workflowhub.eu/workflows/1350?version=1, https://dev.workflowhub.eu/workflows/1370?version=1, https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18, https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=d7c7a4d6c8072167, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.org.au/published/workflow?id=351f3fab960c013b, https://usegalaxy.org/published/workflow?id=2be8ecd5922d23d1, https://workflowhub.eu/workflows/1216?version=1 microbiome/clinical-mp-1-database-generation, proteomics/clinical-mp-1-database-generation
metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function 2018-11-27 https://github.com/galaxyproteomics/metaquantome/ 2.0.2 metaquantome 2.0.2 Up-to-date Proteomics Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 275 283 2663 2893 0 0 0 0 76 76 2011 2011 0 0 0 0 351 1061 4674 14252 https://dev.workflowhub.eu/workflows/1028?version=1, https://dev.workflowhub.eu/workflows/1034?version=1, https://dev.workflowhub.eu/workflows/1155?version=2, https://dev.workflowhub.eu/workflows/1221?version=2, https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba, https://usegalaxy.eu/published/workflow?id=695f7defb516d80d, https://usegalaxy.eu/published/workflow?id=ce7f7c6eef526d67, https://usegalaxy.eu/published/workflow?id=dc438d4ae1866df8, https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9, https://usegalaxy.org.au/published/workflow?id=cada735fa0716570, https://usegalaxy.org.au/published/workflow?id=f8183bba3a1d150d proteomics/metaquantome-function, proteomics/metaquantome-taxonomy
mgf_formatter mgf_formatter 2014-09-26 1.0.0 mgf-formatter 1.0.0 Up-to-date galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mircounts mircounts Generates miRNA count lists from read alignments to mirBase. 2017-06-12 http://artbio.fr 1.6 tar To update RNA, Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 30 30 41 41 1616 1616 0 0 0 0 42 126 1646 4938
misc target_screen, use_theoretical_mz_annotations 2024-02-16 https://github.com/RECETOX/galaxytools 1.0.0 pandas To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 148 148 0 0 0 0 1 1 38 38 0 0 0 0 6 18 186 558 https://workflowhub.eu/workflows/888?version=2
morpheus morpheus Morpheus MS Search Application 2015-10-29 https://cwenger.github.io/Morpheus 288 morpheus 290 To update Proteomics Peptide database search Peptide database search Proteomics Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus morpheus Morpheus A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 13 20 101 177 0 0 0 0 105 105 1020 1020 0 0 0 0 118 361 1121 3439
mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA 2022-03-31 https://github.com/galaxyproteomics/tools-galaxyp/ 0.1.19 bioconductor-preprocesscore 1.68.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3 3 13 13 0 0 0 0 0 0 0 0 0 0 0 0 3 9 13 39
ms2deepscore ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training Mass spectra similarity scoring using a trained ms2deepscore model. 2024-08-15 https://github.com/matchms/ms2deepscore 2.0.0 ms2deepscore 2.5.2 To update Metabolomics Spectrum calculation, Spectral library search, Network analysis Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore ms2deepscore MS2DeepScore MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container 2015-01-24 http://proteowizard.sourceforge.net/tools.shtml 3.0.20287 To update Proteomics Filtering, Formatting Filtering, Formatting Proteomics, Proteomics experiment Proteomics, Proteomics experiment galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 500 525 61681 63743 99 99 1495 1495 61 61 3495 3495 102 102 7131 7131 762 2311 73802 223468 https://dev.workflowhub.eu/workflows/1027?version=1, https://dev.workflowhub.eu/workflows/1031?version=1, https://dev.workflowhub.eu/workflows/1119?version=2, https://dev.workflowhub.eu/workflows/1146?version=3, https://dev.workflowhub.eu/workflows/1177?version=2, https://dev.workflowhub.eu/workflows/1180?version=2, https://dev.workflowhub.eu/workflows/1338?version=1, https://dev.workflowhub.eu/workflows/1354?version=1, https://dev.workflowhub.eu/workflows/1369?version=1, https://dev.workflowhub.eu/workflows/1387?version=1, https://usegalaxy.eu/published/workflow?id=02700454f57eb556, https://usegalaxy.eu/published/workflow?id=14f9c2099db30570, https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9, https://usegalaxy.eu/published/workflow?id=3676aafc35dc2fe7, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=4c81726bde25c36a, https://usegalaxy.eu/published/workflow?id=5d4e4b9f07a1ec20, https://usegalaxy.eu/published/workflow?id=5dec0e5a2d75cdc1, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6b7b86756060659b, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=87c21b682af78ec9, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=9ac15b644c805a2b, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=b73fa5f8c0403454, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=c750484145c9903b, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=d5756e3ebfa285ef, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://usegalaxy.org.au/published/workflow?id=762791e094457bf2, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=8ecc114eb9097855, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1225?version=1 metabolomics/gc_ms_with_xcms, microbiome/clinical-mp-2-discovery, proteomics/DIA_Analysis_OSW, proteomics/clinical-mp-2-discovery, proteomics/encyclopedia, proteomics/metaquantome-data-creation, proteomics/neoantigen-4-peptide-verification, proteomics/protein-id-oms
msgfplus msgfplus MSGF+ 2015-11-10 0.5 msgf_plus 2024.03.26 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 48 736 810 0 0 0 0 0 0 0 0 0 0 0 0 34 116 736 2282
msmetaenhancer msmetaenhancer 2021-11-22 https://github.com/RECETOX/MSMetaEnhancer 0.4.1 msmetaenhancer 0.4.1 Up-to-date Metabolomics Annotation, Standardisation and normalisation Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Metabolomics, Compound libraries and screening, Data submission, annotation and curation recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 209 209 0 0 0 0 1 1 68 68 3 3 10 10 14 42 287 861 https://workflowhub.eu/workflows/888?version=2
msms_extractor msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. 2019-10-23 1.0.0 proteowizard 3_0_9992 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11 12 106 113 0 0 0 0 0 0 0 0 1 1 8 8 12 37 114 349 https://usegalaxy.eu/published/workflow?id=6b7b86756060659b, https://usegalaxy.eu/published/workflow?id=c750484145c9903b
msp_merge msp_merge 2022-05-05 https://github.com/RECETOX/galaxytools 0.1.0 matchms 0.30.0 To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
msstatstmt msstats MSstats tool for analyzing mass spectrometry proteomic datasets 2020-07-25 https://github.com/MeenaChoi/MSstats 4.0.0 bioconductor-msstats 4.14.0 To update Proteomics Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression Proteomics, Proteomics experiment, Protein expression galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 702 702 2789 2789 220 220 1210 1210 36 36 1260 1260 0 0 0 0 958 2874 5259 15777 https://dev.workflowhub.eu/workflows/1026?version=1, https://dev.workflowhub.eu/workflows/1163?version=2, https://dev.workflowhub.eu/workflows/1167?version=2, https://dev.workflowhub.eu/workflows/1240?version=1, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c proteomics/DIA_Analysis_MSstats, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq
msstatstmt msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling 2021-01-20 http://msstats.org/msstatstmt/ 2.0.0 bioconductor-msstatstmt 2.10.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 110 110 826 826 6 6 10 10 16 16 574 574 0 0 0 0 132 396 1410 4230 https://dev.workflowhub.eu/workflows/1227?version=2, https://dev.workflowhub.eu/workflows/1352?version=1, https://dev.workflowhub.eu/workflows/1371?version=1, https://usegalaxy.eu/published/workflow?id=755ede37d94dc456, https://usegalaxy.eu/published/workflow?id=8f3cafa3bc59ff82, https://usegalaxy.eu/published/workflow?id=d148459a4d4b91f1, https://usegalaxy.org.au/published/workflow?id=050a66ff6d4c2b53, https://usegalaxy.org/published/workflow?id=3f797bfb67130883, https://workflowhub.eu/workflows/1219?version=1 microbiome/clinical-mp-5-data-interpretation, proteomics/clinical-mp-5-data-interpretation, proteomics/maxquant-msstats-tmt
mt2mq mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome 2020-06-23 1.1.0 r-tidyverse To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 39 276 276 0 0 0 0 0 0 0 0 0 0 0 0 39 117 276 828
mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs 2020-09-13 http://artbio.fr 3.12.0 bioconductor-mutationalpatterns 3.16.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mz_to_sqlite mz_to_sqlite Creates a SQLite database for proteomics data 2015-06-01 https://github.com/galaxyproteomics/mzToSQLite 2.1.1+galaxy0 mztosqlite 2.1.1 To update Proteomics Conversion, Peptide database search Conversion, Peptide database search Proteomics, Biological databases Proteomics, Biological databases galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite databaseExtract data from proteomics mzIdentML and mass spec scan files: mzML, MGF, etc and store in a SQLite database.The intended purpose is to provide a Galaxy dataset that can support an interactive Galaxy visualization plugin. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 109 112 834 861 16 16 82 82 14 14 296 296 0 0 0 0 139 420 1212 3663 https://dev.workflowhub.eu/workflows/1036?version=1, https://dev.workflowhub.eu/workflows/1151?version=2, https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=2a7e63d1cc583002, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e, https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2 proteomics/proteogenomics-dbsearch
mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. 2023-01-12 https://github.com/RECETOX/galaxytools 0.1.0+galaxy2 lxml To update Metabolomics, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ncbi_blast_plus blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ 2013-09-23 https://blast.ncbi.nlm.nih.gov/ 2.16.0 blast 2.16.0 Up-to-date Sequence Analysis devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 16 16 16 16 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 0 0 0 0 0 16 0 0 0 16 15 16 16 15 0 10892 11931 511765 573432 12429 15085 662235 716213 3431 3994 239169 259544 469 476 11686 11795 27221 85928 1424855 4410694 https://dev.workflowhub.eu/workflows/1043?version=1, https://dev.workflowhub.eu/workflows/1236?version=2, 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assembly/assembly-decontamination, data-science/online-resources-gene, ecology/ENA_Biodiv_submission, ecology/Obitools-metabarcoding, ecology/eDNA-taxonomic-analysis, genome-annotation/functional, proteomics/neoantigen-4-peptide-verification, proteomics/proteogenomics-novel-peptide-analysis, sequence-analysis/Manage_AB1_Sanger, sequence-analysis/ncbi-blast-against-the-madland, sequence-analysis/viral_primer_design
oases oasesoptimiserv Short read assembler 2017-10-15 http://artbio.fr 1.4.0 oases 0.2.09 To update Assembly, RNA artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis 2022-11-04 https://github.com/Marie59/obisindicators 0.0.2 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 357 357 10 10 17 17 0 0 0 0 0 0 0 0 55 165 374 1122 https://dev.workflowhub.eu/workflows/1252?version=2, https://usegalaxy.eu/published/workflow?id=4f51080ffe7d57e0, https://usegalaxy.eu/published/workflow?id=9e05bd65faf58ab3, https://workflowhub.eu/workflows/662?version=1, https://workflowhub.eu/workflows/758?version=1 climate/earth_system, ecology/obisindicators
ocean argo_getdata, copernicusmarine, divand_full_analysis Access, process, and visualise oceanographic data for the Earth System 2023-11-17 https://github.com/Marie59/FE-ft-ESG/tree/main/ocean 0.1.15 copernicusmarine To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 99 99 0 0 0 0 0 0 0 0 0 0 0 0 12 36 99 297 https://dev.workflowhub.eu/workflows/1193?version=1, https://dev.workflowhub.eu/workflows/1200?version=2, https://usegalaxy.eu/published/workflow?id=26fe6b0fb6ca2892, https://usegalaxy.eu/published/workflow?id=a80f9b926ba43892, https://usegalaxy.eu/published/workflow?id=fc33ea1679e5f1b7 climate/argo_pangeo, climate/earth_system, climate/ocean-variables
ocean_data_view_manager tool_biogeochemical_calibration, tool_odv, tool_odv_history The tool merges various datasets with a common vocabulary and creates a single generic ODV spreadsheet in an automatic way. 2025-03-18 https://github.com/Marie59/FE-ft-ESG/tree/main/ocean 1.0 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ocean_neural_network bgc_canyon_b Robust Estimation of Open Ocean CO2 Variables and Nutrient Concentrations From T, S, and O2 Data Using Bayesian Neural Networks 2025-03-18 https://github.com/Marie59/FE-ft-ESG/tree/main/ocean 0.9.3 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_neural_network https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_neural_network 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. 2024-03-12 https://github.com/AquaINFRA/galaxy 1.0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 99 99 0 0 0 0 0 0 0 0 0 0 0 0 7 21 99 297 https://usegalaxy.eu/published/workflow?id=b1fa4a3561988704, https://usegalaxy.eu/published/workflow?id=e8244d1c80ea0470
ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. 2024-03-12 https://github.com/AquaINFRA/galaxy 1.0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 57 57 0 0 0 0 0 0 0 0 0 0 0 0 4 12 57 171 https://usegalaxy.eu/published/workflow?id=e8244d1c80ea0470
omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down 2023-06-23 20230623 fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id 2023-12-22 0.2.0 omero-py 5.11.1 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_get_full_images omero_get_full_images Get full images from omero 2024-05-21 20240521 fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels 2023-03-24 20230809 fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements 2023-03-24 20240214 fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_upload omero_dataset_to_plate, omero_filter, omero_get_id, omero_get_value, omero_import, omero_metadata_import, omero_roi_import Interact with an OMERO.server using omero-py and ezomero. 2024-02-07 https://github.com/ome/omero-py/ 5.18.0 To update Imaging Image analysis Image analysis Imaging, Data visualisation Imaging, Data visualisation ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero omero OMERO Client-server Java software for visualisation, management and analysis of biological microscope images. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://workflowhub.eu/workflows/1258?version=1, https://workflowhub.eu/workflows/1259?version=1 imaging/omero-suite
openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. 2022-03-25 https://github.com/openmm 1.8.1 pdbfixer To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 63 63 1233 1233 0 0 0 0 0 0 0 0 0 0 0 0 63 189 1233 3699
openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses 2017-02-21 https://www.openms.de/ 3.1 openms 3.4.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 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https://dev.workflowhub.eu/workflows/1204?version=2, https://dev.workflowhub.eu/workflows/1213?version=2, https://dev.workflowhub.eu/workflows/1215?version=2, https://dev.workflowhub.eu/workflows/1224?version=2, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=68edbb8eec38ad00, https://usegalaxy.eu/published/workflow?id=7463b26aab6a965d, https://usegalaxy.eu/published/workflow?id=86d50bbaaa3936dc, https://usegalaxy.eu/published/workflow?id=da10c475c83c5469, https://usegalaxy.eu/published/workflow?id=e9e41c23261d4ac5, https://usegalaxy.eu/published/workflow?id=eaf4d8f8fb3e683d, https://usegalaxy.org.au/published/workflow?id=03efeb2948494130, https://usegalaxy.org.au/published/workflow?id=236e0f306916149b, https://usegalaxy.org.au/published/workflow?id=33922db405a97cbb, https://usegalaxy.org.au/published/workflow?id=59c9a6efaf57ce35, https://usegalaxy.org.au/published/workflow?id=65a659982f955743, https://usegalaxy.org.au/published/workflow?id=7cddb345877f08bf, https://usegalaxy.org.au/published/workflow?id=88fa3e250db2d70e, https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5, https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc, https://usegalaxy.org/published/workflow?id=0775ff66d1bc04b5, https://usegalaxy.org/published/workflow?id=9865fee6c68fc201, https://usegalaxy.org/published/workflow?id=f9048d9678e21f36, https://workflowhub.eu/workflows/613?version=2 proteomics/DIA_Analysis_OSW, proteomics/DIA_lib_OSW, proteomics/database-handling, proteomics/ntails, proteomics/protein-id-oms, proteomics/protein-id-sg-ps, proteomics/protein-quant-sil
packmol packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations 2018-10-04 http://m3g.iqm.unicamp.br/packmol/home.shtml 18.169.1 packmol To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 35 269 298 9 9 424 424 0 0 0 0 0 0 0 0 43 130 693 2108
pampa pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics 2020-06-06 0.0.2 To update Ecology ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 154 154 1253 1253 0 0 0 0 42 42 960 960 1 1 1 1 197 591 2214 6642 https://dev.workflowhub.eu/workflows/1283?version=2, https://usegalaxy.eu/published/workflow?id=428be4c7d1fd828f, https://usegalaxy.eu/published/workflow?id=7c45c90fffe40aca, https://usegalaxy.eu/published/workflow?id=d33ab07e4cf44f8c ecology/PAMPA-toolsuite-tutorial
pathifier pathifier pathifier 2019-09-03 https:// 1.40.0 bioconductor-pathifier 1.44.0 To update Transcriptomics, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 257 257 0 0 0 0 0 0 0 0 0 0 0 0 11 33 257 771
pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordinates. 2017-12-19 0.1.3+galaxy1 python To update Genomic Interval Operations, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 56 57 529 545 14 14 23 23 9 9 185 185 0 0 0 0 79 238 737 2227 https://dev.workflowhub.eu/workflows/1043?version=1, https://dev.workflowhub.eu/workflows/1236?version=2, https://dev.workflowhub.eu/workflows/1385?version=2, https://usegalaxy.eu/published/workflow?id=08bbf87ab2a2230e, https://usegalaxy.eu/published/workflow?id=09194b5a549f7979, https://usegalaxy.eu/published/workflow?id=3a178ff6884a5d6d, https://usegalaxy.eu/published/workflow?id=f946efa49bd41a43, https://usegalaxy.org.au/published/workflow?id=c049ae8f729b2d7e, https://usegalaxy.org.au/published/workflow?id=cf5ab8fe4e2c0859, https://usegalaxy.org/published/workflow?id=336d74481d2f721a proteomics/neoantigen-5-variant-annotation, proteomics/proteogenomics-novel-peptide-analysis
pepquery pepquery A peptide-centric MS search engine for novel peptide identification and validation. 2020-01-22 https://pepquery.org 1.6.2 pepquery 2.0.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 76 76 7435 7435 0 0 0 0 0 0 0 0 0 0 0 0 76 228 7435 22305 https://usegalaxy.eu/published/workflow?id=00e246ea459b0991, https://usegalaxy.eu/published/workflow?id=02700454f57eb556, https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=17a1433d0b681d4a, https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=28af61ead68e0976, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=470b629d22b0fc51, https://usegalaxy.eu/published/workflow?id=4c81726bde25c36a, https://usegalaxy.eu/published/workflow?id=58db3e1996a8f093, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6201ec86d380aef1, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6da171871d4f3fd5, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=79eb28066236e836, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=8bb3bc745ea62bed, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=a372f693471beb56, https://usegalaxy.eu/published/workflow?id=adf5e8bead686341, https://usegalaxy.eu/published/workflow?id=b73fa5f8c0403454, https://usegalaxy.eu/published/workflow?id=bfe26679d670bb5e, https://usegalaxy.eu/published/workflow?id=c02ff9e97ce796c6, https://usegalaxy.eu/published/workflow?id=ca342c5018c210e7, https://usegalaxy.eu/published/workflow?id=d5756e3ebfa285ef, https://usegalaxy.eu/published/workflow?id=d95a3349f38792fc, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289
pepquery2 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation 2022-10-02 https://pepquery.org 2.0.2 pepquery 2.0.2 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 3 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 34 34 1649 1649 1 1 1 1 2 2 99 99 0 0 0 0 37 111 1749 5247 https://dev.workflowhub.eu/workflows/1351?version=1, https://dev.workflowhub.eu/workflows/1372?version=1, https://dev.workflowhub.eu/workflows/1382?version=1, https://dev.workflowhub.eu/workflows/1387?version=1, https://usegalaxy.eu/published/workflow?id=5374daf356516a40, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=73dc2384535bf6af, https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d, https://usegalaxy.org.au/published/workflow?id=762791e094457bf2, https://usegalaxy.org.au/published/workflow?id=832a30759469d3fe, https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://usegalaxy.org/published/workflow?id=8ecc114eb9097855, https://usegalaxy.org/published/workflow?id=d0847ce8261eb922, https://workflowhub.eu/workflows/1218?version=1 microbiome/clinical-mp-3-verification, proteomics/clinical-mp-3-verification, proteomics/neoantigen-4-peptide-verification, proteomics/neoantigen-7-hla-binding-novel-peptides
peptide_genomic_coordinate peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files 2019-03-29 1.0.0 python To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 56 56 469 472 11 11 17 17 6 6 171 171 0 0 0 0 73 219 657 1974 https://dev.workflowhub.eu/workflows/1043?version=1, https://dev.workflowhub.eu/workflows/1236?version=2, https://usegalaxy.eu/published/workflow?id=08bbf87ab2a2230e, https://usegalaxy.eu/published/workflow?id=09194b5a549f7979, https://usegalaxy.eu/published/workflow?id=3a178ff6884a5d6d, https://usegalaxy.org.au/published/workflow?id=c049ae8f729b2d7e proteomics/proteogenomics-novel-peptide-analysis
peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI 2015-01-31 http://compomics.github.io searchgui 4.3.14 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 2 0 1088 1219 11820 18426 413 413 1443 1443 130 130 3409 3409 6 6 11 11 1637 5042 16683 56655 https://dev.workflowhub.eu/workflows/1032?version=1, https://dev.workflowhub.eu/workflows/1033?version=1, https://dev.workflowhub.eu/workflows/1036?version=1, https://dev.workflowhub.eu/workflows/1041?version=1, https://dev.workflowhub.eu/workflows/1151?version=2, https://dev.workflowhub.eu/workflows/1159?version=2, https://dev.workflowhub.eu/workflows/1171?version=2, https://dev.workflowhub.eu/workflows/1172?version=2, https://dev.workflowhub.eu/workflows/1177?version=2, https://dev.workflowhub.eu/workflows/1338?version=1, https://dev.workflowhub.eu/workflows/1354?version=1, https://dev.workflowhub.eu/workflows/1369?version=1, https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=0e0be913c3e27022, https://usegalaxy.eu/published/workflow?id=1706bfa819bbfa89, https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=249c7569b61fb349, https://usegalaxy.eu/published/workflow?id=2a7e63d1cc583002, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=4c81726bde25c36a, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6766bed39f614b7c, https://usegalaxy.eu/published/workflow?id=68967c922de149ae, https://usegalaxy.eu/published/workflow?id=6aca8a72626c521b, https://usegalaxy.eu/published/workflow?id=6b7b86756060659b, https://usegalaxy.eu/published/workflow?id=6bd8311554412c38, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=7463b26aab6a965d, https://usegalaxy.eu/published/workflow?id=78e1769f1dcb797b, https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=8fc1ea9e94bc723d, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=9c0132dd81297afe, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=a4d6b9dc6b396933, https://usegalaxy.eu/published/workflow?id=a657b412b37b971b, https://usegalaxy.eu/published/workflow?id=b73fa5f8c0403454, https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=c750484145c9903b, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=d1d5a6bd6571d47f, https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2, https://usegalaxy.eu/published/workflow?id=d5756e3ebfa285ef, https://usegalaxy.eu/published/workflow?id=d9e7a940b2d410bc, https://usegalaxy.eu/published/workflow?id=df926c5ab8d27192, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=f34c76e2d8045725, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2, https://usegalaxy.org.au/published/workflow?id=33922db405a97cbb, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5, https://usegalaxy.org.au/published/workflow?id=f9f685d6150e48c5, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1225?version=1 microbiome/clinical-mp-2-discovery, proteomics/clinical-mp-2-discovery, proteomics/metaproteomics, proteomics/metaquantome-data-creation, proteomics/protein-id-sg-ps, proteomics/proteogenomics-dbsearch
pepxml_to_xls Convert PepXML to Tabular 2015-01-24 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
percolator batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator 2016-04-12 3.5 percolator 3.7.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 15 16 268 378 0 0 0 0 13 13 1251 1251 0 0 0 0 28 85 1519 4667
phabox phabox_cherry, phabox_contamination, phabox_end_to_end, phabox_phagcn, phabox_phamer, phabox_phatyp, phabox_phavip, phabox_tree, phabox_votu Identify and analyze phage contigs in metagenomic data 2024-11-12 https://github.com/KennthShang/PhaBOX 2.1.11 phabox 2.1.11 Up-to-date Metagenomics Sequence assembly, Taxonomic classification, Visualisation Sequence assembly, Taxonomic classification, Visualisation Metagenomics, Microbial ecology, Sequence assembly, Taxonomy Metagenomics, Microbial ecology, Sequence assembly, Taxonomy ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phabox phabox PhaBOX Web server for identifying and characterizing phage contigs in metagenomic data. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
phi_toolkit_report phi_toolkit_report Phage host interaction toolkit report generator 2025-06-04 https://git.ufz.de/borimcor/phage-host-analysis 0.1.0 bioconductor-biostrings 2.74.0 To update Metagenomics ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phi-toolkit 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pindel pindel Pindel detects genome-wide structural variation. 2021-09-29 http://artbio.fr 0.2.5b9 pindel 0.2.5b9 Up-to-date Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plot_tools_astro_tool plot_tools_astro_tool Plot Tools 2024-11-22 0.0.1+galaxy0 pandas To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/plot-tools 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS 2019-10-01 https://github.com/slhubler/PMD-FDR-for-Galaxy-P 1.4.0 r-base To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. 2016-11-04 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Variant Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. 2016-11-07 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Variant Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets 2017-09-22 http://artbio.fr 0.22.0 pysam 0.23.2 To update Sequence Analysis, Genomic Interval Operations, Graphics, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml 2015-01-24 0.1 To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
proteomics_moff proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. 2017-12-11 https://github.com/compomics/moFF 2.0.3 moff 2.0.3 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 19 35 343 787 0 0 0 0 4 4 157 157 0 0 0 0 23 85 500 1944
proteomiqon_joinquantpepionswithproteins proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. 2021-09-16 https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 372 372 0 0 0 0 0 0 0 0 0 0 0 0 5 15 372 1116
proteomiqon_labeledproteinquantification proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. 2021-09-16 https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 16 16 0 0 0 0 0 0 0 0 0 0 0 0 8 24 16 48
proteomiqon_labelfreeproteinquantification proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. 2021-10-13 https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 8 8 0 0 0 0 0 0 0 0 0 0 0 0 6 18 8 24
proteomiqon_mzmltomzlite proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. 2021-06-30 https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html 0.0.8 proteomiqon-mzmltomzlite 0.0.8 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 722 722 0 0 0 0 0 0 0 0 0 0 0 0 9 27 722 2166
proteomiqon_peptidedb proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. 2021-07-04 https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html 0.0.7 proteomiqon-peptidedb 0.0.7 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 96 96 0 0 0 0 0 0 0 0 0 0 0 0 12 36 96 288
proteomiqon_peptidespectrummatching proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. 2021-07-15 https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 686 686 0 0 0 0 0 0 0 0 0 0 0 0 5 15 686 2058
proteomiqon_proteininference proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. 2021-07-09 https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html 0.0.7 proteomiqon-proteininference 0.0.7 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 89 89 0 0 0 0 0 0 0 0 0 0 0 0 6 18 89 267
proteomiqon_psmbasedquantification proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. 2021-07-09 https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html 0.0.8 proteomiqon-psmbasedquantification 0.0.9 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 604 604 0 0 0 0 0 0 0 0 0 0 0 0 4 12 604 1812
proteomiqon_psmstatistics proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. 2021-07-09 https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html 0.0.8 proteomiqon-psmstatistics 0.0.8 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 694 694 0 0 0 0 0 0 0 0 0 0 0 0 6 18 694 2082
proteore_venn_diagram proteore_venn_diagram ProteoRE JVenn Diagram 2021-05-17 2021.06.08 python To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 15 15 0 0 0 0 0 0 0 0 0 0 0 0 1 3 15 45
protxml_to_xls protxml_to_xls 2015-01-24 0.1.0 trans_proteomic_pipeline To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
psm_eval psm_eval 2015-01-24 0.1.0 binaries_for_psm_eval To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
psm_to_sam PSMtoSAM PSM to SAM 2017-10-06 https://bioconductor.org/packages/release/bioc/html/proBAMr.html 1.3.2.1 r-base To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
psm_validation psmvalidator Validate PSM from Ion Fragmentation 2020-10-13 https://github.com/galaxyproteomics/psm_fragments.git 1.0.3 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 20 20 0 0 0 0 0 0 0 0 0 0 0 0 4 12 20 60
psy_maps psy_maps Visualization of regular geographical data on a map with psyplot 2019-03-15 https://github.com/Chilipp/psy-maps 1.3.1 python To update Visualization, Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 68 68 367 557 0 0 0 0 0 0 0 0 0 0 0 0 68 204 367 1291 https://dev.workflowhub.eu/workflows/1138?version=2, https://usegalaxy.eu/published/workflow?id=21363a774a7575f0, https://usegalaxy.eu/published/workflow?id=392a5d91ac221104, https://usegalaxy.eu/published/workflow?id=6df53b44018b2235 climate/climate-101
ptxqc maxquant_ptxqc Quality control reports for MaxQuant results 2025-04-16 https://github.com/cbielow/PTXQC 1.1.2 r-ptxqc To update Proteomics Validation Validation Proteomics Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ptxqc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ptxqc ptxqc PTXQC PTXQC is a quality control pipeline for proteomics results generated by MaxQuant. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. 2015-02-06 https://github.com/PyProphet/pyprophet 2.1.4 pyprophet 2.2.5 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 0 5 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 6 6 0 150 150 2626 2626 0 0 0 0 10 10 809 809 0 0 0 0 160 480 3435 10305 https://dev.workflowhub.eu/workflows/1031?version=1, https://dev.workflowhub.eu/workflows/1180?version=2 proteomics/DIA_Analysis_OSW
pyteomics mztab2tsv Tools using the pyteomics library 2021-01-15 https://pyteomics.readthedocs.io/en/latest/ 4.4.1 pyteomics 4.7.5 To update Proteomics, Metabolomics Protein identification Protein identification Proteomics, Proteomics experiment Proteomics, Proteomics experiment galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 92 92 0 0 0 0 0 0 0 0 0 0 0 0 4 12 92 276
quantp quantp Correlation between protein and transcript abundance 2018-09-13 1.1.2 r-data.table 1.11.6 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 17 23 165 242 0 0 0 0 0 0 0 0 0 0 0 0 17 57 165 572
quantwiz_iq quantwiz_iq Isobaric Quantitation using QuantWiz-IQ 2020-01-21 https://sourceforge.net/projects/quantwiz/ 2.0 quantwiz-iq 2.0 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3 3 29 32 0 0 0 0 0 0 0 0 0 0 0 0 3 9 29 90
query query Execute an SQL statement on a set of tables 2020-12-09 0.2 click To update Text Manipulation recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query https://github.com/RECETOX/galaxytools/tree/master/tools/query 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
qupath_roi_splitter qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type 2023-04-12 https://github.com/npinter/ROIsplitter 0.3.2 geojson To update Imaging galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 181 181 0 0 0 0 0 0 0 0 0 0 0 0 9 27 181 543
ramclustr ramclustr, ramclustr_define_experiment 2020-11-05 https://rdrr.io/cran/RAMClustR/ 1.3.0 r-ramclustr 1.3.1 To update Metabolomics Imputation, Standardisation and normalisation, Clustering, Correlation Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 26 26 71 71 15 15 31 31 4 4 500 500 38 38 257 257 83 249 859 2577 https://dev.workflowhub.eu/workflows/1119?version=2, https://usegalaxy.eu/published/workflow?id=3086366b744e8da9, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07 metabolomics/gc_ms_with_xcms
rawtools rawtools Raw Tools 2019-02-28 https://github.com/kevinkovalchik/RawTools rawtools 2.0.4 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 36 137 183 0 0 0 0 15 15 477 477 0 0 0 0 48 147 614 1888
rcx_boxplot rcx_boxplot recetox-boxplot is a tool for plotting boxplots from a tabular/csv/parquet data file. 2025-01-31 https://github.com/RECETOX/galaxytools 3.5.1 r-ggplot2 2.2.1 To update Visualization recetox https://github.com/RECETOX/galaxytools/tree/master/tools https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_boxplot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rcx_tk rcx-tk Tools to process metadata or alkane files. 2024-08-01 https://github.com/RECETOX/rcx-tk 0.1.0 rcx-tk 0.1.0 Up-to-date Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
reactome_pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher 2018-06-08 https://github.com/LuisFranciscoHS/PathwayMatcher pathwaymatcher 1.9.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 66 83 165 258 0 0 0 0 0 0 0 0 0 0 0 0 66 215 165 588
recetox-aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. 2021-06-17 https://github.com/RECETOX/recetox-aplcms 0.13.4 r-recetox-aplcms 0.13.4 Up-to-date Metabolomics Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. 0 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 24 24 1508 1508 0 0 0 0 8 8 202 202 11 11 928 928 43 129 2638 7914 https://usegalaxy.eu/published/workflow?id=3086366b744e8da9
recetox-msfinder recetox_msfinder 2022-11-28 https://github.com/RECETOX/recetox-msfinder v3.5.2 To update Metabolomics Annotation Annotation Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 70 70 0 0 0 0 1 1 57 57 7 7 19 19 15 45 146 438 https://workflowhub.eu/workflows/888?version=2
recetox-xmsannotator recetox_xmsannotator_advanced 2021-07-13 https://github.com/RECETOX/recetox-xMSannotator 0.10.0 r-recetox-xmsannotator 0.10.0 Up-to-date Metabolomics Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 2 2 133 133 0 0 0 0 2 6 133 399
regex_find_replace regex1, regexColumn1 Use python regular expressions to find and replace text 2017-01-13 1.0.3 python To update Text Manipulation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 2 2 2 0 1344 1390 89919 90483 1000 1000 19509 19509 191 314 4680 6501 49 49 569 569 2584 7921 114677 346416 https://dev.workflowhub.eu/workflows/1001?version=1, https://dev.workflowhub.eu/workflows/1042?version=1, https://dev.workflowhub.eu/workflows/1077?version=2, https://dev.workflowhub.eu/workflows/1083?version=1, https://dev.workflowhub.eu/workflows/1087?version=2, https://dev.workflowhub.eu/workflows/1090?version=2, https://dev.workflowhub.eu/workflows/1096?version=2, https://dev.workflowhub.eu/workflows/1173?version=2, https://dev.workflowhub.eu/workflows/1177?version=2, 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https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=6d778eeb176d563c, https://usegalaxy.org/published/workflow?id=76b2c4762dd61d03, https://usegalaxy.org/published/workflow?id=b28789b6a0e1f5c9, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://usegalaxy.org/published/workflow?id=fbf75fbb72b488bd, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1063?version=3, https://workflowhub.eu/workflows/117?version=1, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/1208?version=1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/363?version=2, https://workflowhub.eu/workflows/660?version=1 climate/pangeo, data-science/data-manipulation-olympics, ecology/ENA_Biodiv_submission, ecology/Ecoregionalization_tutorial, ecology/PAMPA-toolsuite-tutorial, ecology/biodiversity-data-exploration, ecology/ecoregiolifetraits, ecology/marine_omics_bgc, ecology/openrefine_gbif, ecology/phylogeny-data-prep, ecology/regionalGAM, genome-annotation/gene-centric, introduction/data-manipulation-olympics, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/metaquantome-data-creation, proteomics/neoantigen-1-fusion-database-generation, proteomics/neoantigen-2-non-reference-database-generation, proteomics/neoantigen-5-variant-annotation, proteomics/proteogenomics-dbcreation, sequence-analysis/Manage_AB1_Sanger, single-cell/EBI-retrieval, single-cell/bulk-music-2-preparescref, single-cell/bulk-music-3-preparebulk, single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-data-ingest, variant-analysis/trio-analysis
regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend 2019-06-18 https://github.com/RetoSchmucki/regionalGAM 1.5 r-mgcv To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 7 0 132 161 374 546 0 0 0 0 0 0 0 0 0 0 0 0 132 425 374 1294 https://dev.workflowhub.eu/workflows/1222?version=1, https://usegalaxy.eu/published/workflow?id=8e92a65d3307d87e ecology/regionalGAM
rem_complex rem_complex Removes molecular coordination complexes. 2023-11-21 https://github.com/RECETOX/galaxytools 1.0.0 pandas To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 23 23 0 0 0 0 1 1 76 76 0 0 0 0 3 9 99 297 https://workflowhub.eu/workflows/888?version=2
rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results 2024-05-13 https://github.com/RECETOX/galaxytools/ 1.0.0 pandas To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 1 1 38 38 0 0 0 0 3 9 40 120 https://usegalaxy.eu/published/workflow?id=3086366b744e8da9
repenrich edger-repenrich, repenrich Repeat element profiling 2017-05-22 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 To update Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 59 61 1794 1935 0 0 0 0 59 179 1794 5523
repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner 2024-04-20 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 To update Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
retip retip_apply, retip_descriptors, retip_filter_rt, retip_train 2020-09-07 https://github.com/PaoloBnn/Retip 0.5.4 To update Metabolomics Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
retrieve_bold retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers 2024-06-21 https://anaconda.org/conda-forge/r-bold 1.3.0 r-base To update Ecology ecology https://github.com/wpearman1996/MARES_database_pipeline/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 10 10 0 0 0 0 0 0 0 0 0 0 0 0 4 12 10 30
retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format 2018-01-14 http://rest.ensembl.org/ 0.1.0 To update Data Source galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
revertr2orientationinbam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. 2019-04-17 0.0.2 samtools 1.22 To update SAM lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 40 40 32 32 538 538 0 0 0 0 0 0 0 0 43 129 578 1734 https://usegalaxy.eu/published/workflow?id=6ebd09100fc98878, https://usegalaxy.eu/published/workflow?id=c98a14fcf5998159, https://usegalaxy.eu/published/workflow?id=d3494c6124f820b2, https://usegalaxy.eu/published/workflow?id=ef1d11b79a2e1727, https://usegalaxy.eu/published/workflow?id=fa53b172def3fe75, https://usegalaxy.org.au/published/workflow?id=5cd9b9338e75f254, https://usegalaxy.org/published/workflow?id=1f28e673ea725541, https://usegalaxy.org/published/workflow?id=53fdff74729a6780, https://usegalaxy.org/published/workflow?id=778a8867b0a6ea4f, https://usegalaxy.org/published/workflow?id=868acaf49d0743ec, https://usegalaxy.org/published/workflow?id=93e69c7e7a857ca3, https://usegalaxy.org/published/workflow?id=f3c8093c5b8a7233, https://workflowhub.eu/workflows/401?version=13
riassigner riassigner, riassigner_from_comment 2021-08-19 https://github.com/RECETOX/RIAssigner 0.4.1 riassigner 0.4.1 Up-to-date Metabolomics Standardisation and normalisation Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Metabolomics, Compound libraries and screening, Data submission, annotation and curation recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. 1 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 23 23 59 59 5 5 16 16 2 2 77 77 24 24 150 150 54 162 302 906 https://dev.workflowhub.eu/workflows/1119?version=2, https://usegalaxy.eu/published/workflow?id=3086366b744e8da9, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07 metabolomics/gc_ms_with_xcms
rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. 2021-02-25 https://github.com/MassBank/RMassBank 3.0.0 python To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 68 68 0 0 0 0 1 3 68 204
rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data 2017-12-18 https://github.com/deweylab/RSEM rsem 1.3.3 To update Transcriptomics, RNA artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 1 1 0 161 196 361 460 0 0 0 0 10 39 48 146 0 0 0 0 171 577 409 1424
salmon_kallisto_mtx_to_10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data 2019-11-07 https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary 0.0.1+galaxy6 scipy To update Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 219 219 788 791 82 82 345 345 3 3 3 3 0 0 0 0 304 912 1136 3411 https://dev.workflowhub.eu/workflows/1024?version=1, https://dev.workflowhub.eu/workflows/1025?version=1, https://dev.workflowhub.eu/workflows/1263?version=1, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=9ed36a6849fa2014, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d single-cell/scrna-case_alevin
sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM 2020-05-19 http://artbio.fr 0.7.1+galaxy1 sambamba 1.0.1 To update SAM artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 836 836 0 0 0 0 21 63 836 2508
saqc saqc System for automated Quality Control 2025-01-13 https://git.ufz.de/rdm-software/saqc 2.4.1 saqc To update Statistics ufz https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/saqc 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sashimi_plot sashimi_plot Generates a sashimi plot from bam files. 2019-08-21 http://artbio.fr 0.1.1 python To update RNA, Transcriptomics, Graphics, Visualization artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
scaffold scaffold, scaffold_export 2015-01-24 0.1.0 scaffold To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
scanpy_scripts anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. 2018-11-05 https://scanpy.readthedocs.io 1.9.3 scanpy-scripts 1.9.301 To update Transcriptomics, Sequence Analysis, RNA ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 14 13 0 5943 6062 51597 52275 2082 2082 8511 8511 468 468 3203 3203 0 0 0 0 8493 25598 63311 190611 https://dev.workflowhub.eu/workflows/1014?version=1, https://dev.workflowhub.eu/workflows/1015?version=1, https://dev.workflowhub.eu/workflows/1016?version=1, https://dev.workflowhub.eu/workflows/1017?version=1, https://dev.workflowhub.eu/workflows/1021?version=1, https://dev.workflowhub.eu/workflows/1023?version=1, https://dev.workflowhub.eu/workflows/1210?version=2, https://dev.workflowhub.eu/workflows/1212?version=1, https://dev.workflowhub.eu/workflows/1219?version=2, https://dev.workflowhub.eu/workflows/1225?version=1, https://dev.workflowhub.eu/workflows/1238?version=1, https://dev.workflowhub.eu/workflows/1243?version=2, https://dev.workflowhub.eu/workflows/1246?version=2, https://dev.workflowhub.eu/workflows/1261?version=1, https://dev.workflowhub.eu/workflows/1272?version=2, https://dev.workflowhub.eu/workflows/1343?version=2, https://dev.workflowhub.eu/workflows/1377?version=1, https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=0909859a02040efc, https://usegalaxy.eu/published/workflow?id=0d7c643d7720ee31, https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=171d6fca2c3339e2, https://usegalaxy.eu/published/workflow?id=1d4e81b51eae43c4, https://usegalaxy.eu/published/workflow?id=37e51e215684bdcc, https://usegalaxy.eu/published/workflow?id=50f8693fac7e134b, https://usegalaxy.eu/published/workflow?id=5b8e4ae3447934d9, https://usegalaxy.eu/published/workflow?id=715ca378c1d68de3, https://usegalaxy.eu/published/workflow?id=71f7725b261c6c83, https://usegalaxy.eu/published/workflow?id=73aa794916b91bb2, https://usegalaxy.eu/published/workflow?id=73b41b975da284d5, https://usegalaxy.eu/published/workflow?id=78dc6fca5b58ec05, https://usegalaxy.eu/published/workflow?id=8ce45d9ca1b62624, https://usegalaxy.eu/published/workflow?id=8f677efac7100097, https://usegalaxy.eu/published/workflow?id=9a0275211e74698a, https://usegalaxy.eu/published/workflow?id=9a7d8552f5774fbd, https://usegalaxy.eu/published/workflow?id=ae79275d3568ad31, https://usegalaxy.eu/published/workflow?id=aeb0f5b74e51f5c2, https://usegalaxy.eu/published/workflow?id=b3cf397fd4d1bea8, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=d7c0c972c471d514, https://usegalaxy.eu/published/workflow?id=decd6ad0b41289ef, https://usegalaxy.eu/published/workflow?id=e2391c40d24d403f, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://usegalaxy.eu/published/workflow?id=e97bdba3834ac465, https://usegalaxy.eu/published/workflow?id=ea102016a86c3eff, https://usegalaxy.eu/published/workflow?id=ebfd7cabc0dc97f8, https://usegalaxy.eu/published/workflow?id=f05754467a439134, https://usegalaxy.eu/published/workflow?id=f27abf3c623d3062, https://usegalaxy.eu/published/workflow?id=ffbbb905164d4c11, https://usegalaxy.org/published/workflow?id=802f5ff14a924e42, https://usegalaxy.org/published/workflow?id=dd43ae9a5b303086, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/467?version=4, https://workflowhub.eu/workflows/468?version=3, https://workflowhub.eu/workflows/512?version=2, https://workflowhub.eu/workflows/513?version=3, https://workflowhub.eu/workflows/646?version=2 imaging/multiplex-tissue-imaging-TMA, single-cell/EBI-retrieval, single-cell/bulk-music-2-preparescref, single-cell/scanpy_parameter_iterator, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_alevin-combine-datasets, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_cell-cycle, single-cell/scrna-case_trajectories, single-cell/scrna-data-ingest, single-cell/scrna-ncbi-anndata
sceasy sceasy_convert Convert scRNA data object between popular formats 2019-10-14 0.0.5 r-sceasy 0.0.7 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 286 286 1379 1381 83 83 470 470 3 3 147 147 0 0 0 0 372 1116 1996 5990 https://dev.workflowhub.eu/workflows/1024?version=1, https://dev.workflowhub.eu/workflows/1025?version=1, https://dev.workflowhub.eu/workflows/1263?version=1, https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=9ed36a6849fa2014, https://usegalaxy.eu/published/workflow?id=a0f1959a9f4533f7, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d single-cell/EBI-retrieval, single-cell/scrna-case_alevin, single-cell/scrna-data-ingest
scripting tools singularity_scriptrunner suite_scripting 2023-07-29 https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ 0.2 To update Text Manipulation mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. 2024-03-29 https://cran.r-project.org/web/packages/sdmpredictors/index.html 0.2.15 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3 3 0 0 0 0 0 0 0 0 0 0 0 0 2 6 3 9
sequence_format_converter sequence_format_converter various fasta to tabular conversions 2017-09-04 http://artbio.fr 2.2.0 python To update Convert Formats, Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sgwb_astro_tool sgwb_astro_tool SGWB 2024-04-17 0.0.1+galaxy0 ipython To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 7 7 0 0 0 0 0 0 0 0 0 0 0 0 3 9 7 21 https://workflowhub.eu/workflows/815?version=2, https://workflowhub.eu/workflows/831?version=1
shift_longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees 2019-03-15 https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ 0.1.0 python To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 5 54 80 0 0 0 0 0 0 0 0 0 0 0 0 5 15 54 188
sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS 2016-10-11 0.2.4 sixgill 0.2.4 Up-to-date Proteomics, MetaProteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 74 74 316 316 0 0 0 0 0 0 0 0 0 0 0 0 74 222 316 948 https://usegalaxy.eu/published/workflow?id=799b924edd3c401b
small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files 2019-10-06 http://artbio.fr 1.3.0 pysam 0.23.2 To update RNA, SAM, Graphics, Next Gen Mappers artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
small_rna_maps small_rna_maps Generates small read maps from alignment BAM files 2017-07-23 http://artbio.fr 3.1.1 numpy To update RNA, SAM, Graphics, Next Gen Mappers artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. 2017-08-28 http://artbio.fr 3.4.2 pysam 0.23.2 To update RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
smithsonian_volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database 2019-04-15 https://volcano.si.edu/gvp_votw.cfm 0.1.0 python To update Retrieve Data climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
snv_matrix snvmatrix Generate matrix of SNV distances 2016-01-21 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza 2021-03-07 http://artbio.fr 3.0.0+galaxy1 sequenza-utils 3.0.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. 2022-11-29 https://github.com/iomega/spec2vec 0.8.0 spec2vec 0.8.0 Up-to-date Metabolomics Spectrum calculation, Spectral library search, Database search, Natural product identification Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Proteomics experiment, Metabolomics, Natural language processing, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 2 2 114 114 0 0 0 0 3 9 115 345
spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files 2015-04-13 0.1.0 msproteomicstools 0.11.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files 2015-02-06 0.1.0 msproteomicstools 0.11.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spocc_occ spocc_occ Get species occurences data 2019-05-23 https://cran.r-project.org/web/packages/spocc/index.html 1.2.2 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 126 140 732 896 0 0 0 0 0 0 0 0 11 11 19 19 137 425 751 2417 https://dev.workflowhub.eu/workflows/1235?version=1, https://dev.workflowhub.eu/workflows/1268?version=2, https://usegalaxy.eu/published/workflow?id=3b0803542deff026, https://usegalaxy.eu/published/workflow?id=b0b6c8756070650b, https://workflowhub.eu/workflows/404?version=1 climate/earth_system, ecology/gbif_cleaning, ecology/species-distribution-modeling
sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads 2017-09-02 http://artbio.fr 2.3.1 bowtie 1.3.1 To update RNA, Next Gen Mappers Microbiology, Biology Microbiology artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie sr_bowtie sr_bowtie Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25... _Bowtie: http://bowtie-bio.sourceforge.net/index.shtmlA generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.However, this Bowtie wrapper tool only takes FASTQ files as inputs.The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 98 98 0 0 0 0 0 0 0 0 2 6 98 294
sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. 2017-09-11 http://artbio.fr 2.8 bowtie 1.3.1 To update RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 2022-11-16 0.0.1 r-base To update Ecology ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 4 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 35 35 255 255 13 13 44 44 0 0 0 0 4 4 16 16 52 156 315 945 https://dev.workflowhub.eu/workflows/1211?version=1, https://usegalaxy.eu/published/workflow?id=1d2cd0af01a30a46, https://usegalaxy.eu/published/workflow?id=da88448ab15d167d, https://workflowhub.eu/workflows/657?version=1 ecology/remote-sensing
stoceps stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. 2019-09-26 0.0.2 To update Ecology ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 45 45 338 338 0 0 0 0 0 0 0 0 0 0 0 0 45 135 338 1014 https://usegalaxy.eu/published/workflow?id=01274dfdbdfcaa88
suite_cell_types_analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis 2020-04-07 1.1.1 cell-types-analysis 0.1.11 To update Transcriptomics, RNA, Statistics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 9 9 0 0 0 0 0 0 0 0 0 0 0 0 5 15 9 27 https://usegalaxy.eu/published/workflow?id=4091c0e2b471fc92, https://usegalaxy.eu/published/workflow?id=6a2c373b3b5d97df, https://usegalaxy.eu/published/workflow?id=a496111beb6e23d0, https://usegalaxy.eu/published/workflow?id=d9e9424dd755729d
suite_celltypist celltypist_predict celltypist - Automated cell type annotation 2025-02-14 https://celltypist.readthedocs.io/en/latest/ 1.6.3+galaxy1 celltypist 1.6.3 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/celltypist 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities 2023-09-24 https://decoupler-py.readthedocs.io/en/latest/ 1.4.0+galaxy3 decoupler 1.5.0 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 120 120 1 1 2 2 0 0 0 0 0 0 0 0 10 30 122 366 https://dev.workflowhub.eu/workflows/1395?version=1, https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809, https://usegalaxy.eu/published/workflow?id=d1b3b62e7f91e217, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.org/published/workflow?id=13a3954b8894e1b1, https://workflowhub.eu/workflows/1207?version=2 single-cell/pseudobulk-analysis
suite_dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 2019-01-22 1.0.4 dropletutils-scripts 0.0.5 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 513 515 2123 2133 154 154 679 679 1 1 1 1 0 0 0 0 668 2006 2803 8419 https://dev.workflowhub.eu/workflows/1020?version=1, https://dev.workflowhub.eu/workflows/1024?version=1, https://dev.workflowhub.eu/workflows/1025?version=1, https://dev.workflowhub.eu/workflows/1247?version=2, https://dev.workflowhub.eu/workflows/1263?version=1, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=4091c0e2b471fc92, https://usegalaxy.eu/published/workflow?id=49a6ddcba35bf085, https://usegalaxy.eu/published/workflow?id=6a2c373b3b5d97df, https://usegalaxy.eu/published/workflow?id=95fe49cafa1dff7e, https://usegalaxy.eu/published/workflow?id=9ed36a6849fa2014, https://usegalaxy.eu/published/workflow?id=a496111beb6e23d0, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=dc9bfa4f633c49b4, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f474eb2f45f1d684, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d single-cell/scrna-case_alevin, single-cell/scrna-data-ingest
suite_ebi_expression_atlas retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home 2019-07-02 v0.0.2+galaxy2 wget To update Transcriptomics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 284 290 1201 1235 116 116 384 384 11 11 113 113 3 3 6 6 414 1248 1704 5146 https://dev.workflowhub.eu/workflows/1023?version=1, https://dev.workflowhub.eu/workflows/1210?version=2, https://dev.workflowhub.eu/workflows/1257?version=1, https://dev.workflowhub.eu/workflows/1261?version=1, https://dev.workflowhub.eu/workflows/1375?version=1, https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=0909859a02040efc, https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=1d4e81b51eae43c4, https://usegalaxy.eu/published/workflow?id=290373b2f5fb8c6c, https://usegalaxy.eu/published/workflow?id=5d31bafd82547d5d, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=dd73bdcbac8649a3, https://usegalaxy.eu/published/workflow?id=e2391c40d24d403f, https://usegalaxy.eu/published/workflow?id=ea102016a86c3eff, https://usegalaxy.eu/published/workflow?id=ebfd7cabc0dc97f8, https://usegalaxy.eu/published/workflow?id=f05754467a439134 single-cell/EBI-retrieval, single-cell/bulk-music-2-preparescref, single-cell/scrna-case_FilterPlotandExplore_SeuratTools, single-cell/scrna-case_basic-pipeline
suite_garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 2020-04-03 0.2.8 garnett-cli 0.0.5 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11 27 27 0 0 0 0 0 0 0 0 0 0 0 0 11 33 27 81 https://usegalaxy.eu/published/workflow?id=8762437178c9a3cf, https://usegalaxy.eu/published/workflow?id=d9e9424dd755729d
suite_human_cell_atlas_tools hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects 2019-07-02 v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 To update Transcriptomics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 100 111 522 556 2 2 3 3 0 0 0 0 0 0 0 0 102 317 525 1609 https://usegalaxy.eu/published/workflow?id=71f7725b261c6c83 single-cell/EBI-retrieval
suite_monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. 2019-09-09 0.1.4 monocle3-cli 0.0.9 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 577 577 3665 3665 454 454 1816 1816 0 0 0 0 0 0 0 0 1031 3093 5481 16443 https://dev.workflowhub.eu/workflows/1018?version=1, https://dev.workflowhub.eu/workflows/1228?version=1, https://dev.workflowhub.eu/workflows/1237?version=1, https://dev.workflowhub.eu/workflows/1251?version=2, https://usegalaxy.eu/published/workflow?id=35c092316cdc27d1, https://usegalaxy.eu/published/workflow?id=8762437178c9a3cf, https://usegalaxy.eu/published/workflow?id=a3a7c1853ae7047b, https://usegalaxy.eu/published/workflow?id=a7fcfab658a2cc33, https://usegalaxy.eu/published/workflow?id=d9e9424dd755729d, https://usegalaxy.eu/published/workflow?id=f689faf267fbe504 single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-data-ingest
suite_ogs ogs_addlayer, ogs_extractboundary, ogs_extractsurface, ogs_generatestructuredmesh, ogs_identifysubdomains, ogs_simulation A suite of tools for OpenGeoSys (ogs) 2025-03-06 https://gitlab.opengeosys.org/ogs/ogs 6.5.3 To update Geo Science ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_ogs_tools msh2vtu, shp2msh A suite of tools for OpenGeoSys (ogs) 2025-03-03 https://gitlab.opengeosys.org/ogs/tools/ogstools 0.4.0 ogstools To update Geo Science ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogstools https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogstools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ 2024-08-20 0.12.1 To update Transcriptomics, RNA, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. 2018-11-05 1.8.0 sc3-scripts 0.0.6 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 10 11 13 0 0 0 0 0 0 0 0 0 0 0 0 8 26 11 35
suite_scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. 2018-10-11 1.10.0 scater-scripts 0.0.5 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 97 104 343 397 0 0 0 0 9 9 360 360 0 0 0 0 106 325 703 2163 https://dev.workflowhub.eu/workflows/1241?version=2, https://usegalaxy.eu/published/workflow?id=f055b8fa294d4be8, https://usegalaxy.org.au/published/workflow?id=3c9140288202aa76 single-cell/scrna-scater-qc
suite_scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. 2019-08-30 1.6.4 scmap-cli 0.1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 41 41 114 114 0 0 0 0 0 0 0 0 0 0 0 0 41 123 114 342 https://usegalaxy.eu/published/workflow?id=6a2c373b3b5d97df, https://usegalaxy.eu/published/workflow?id=95fe49cafa1dff7e, https://usegalaxy.eu/published/workflow?id=a496111beb6e23d0, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=dc9bfa4f633c49b4
suite_scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 2020-04-07 1.0.2 scpred-cli 0.1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 25 25 0 0 0 0 0 0 0 0 0 0 0 0 5 15 25 75 https://usegalaxy.eu/published/workflow?id=4091c0e2b471fc92, https://usegalaxy.eu/published/workflow?id=f474eb2f45f1d684
suite_seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 2018-07-09 https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 4.0.0 seurat-scripts 4.4.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 833 892 3628 3786 488 488 1776 1776 17 17 188 188 15 15 45 45 1353 4118 5637 17069 https://dev.workflowhub.eu/workflows/1019?version=1, https://dev.workflowhub.eu/workflows/1210?version=2, https://dev.workflowhub.eu/workflows/1255?version=2, https://dev.workflowhub.eu/workflows/1375?version=1, https://dev.workflowhub.eu/workflows/1388?version=1, https://dev.workflowhub.eu/workflows/1389?version=1, https://usegalaxy.eu/published/workflow?id=0909859a02040efc, https://usegalaxy.eu/published/workflow?id=10c5d0560b977a6f, https://usegalaxy.eu/published/workflow?id=26deb6f2521742ea, https://usegalaxy.eu/published/workflow?id=290373b2f5fb8c6c, https://usegalaxy.eu/published/workflow?id=5d31bafd82547d5d, https://usegalaxy.eu/published/workflow?id=704e6c9bc51db49f, https://usegalaxy.eu/published/workflow?id=a0f1959a9f4533f7, https://usegalaxy.eu/published/workflow?id=c52e8b5ab3e8e958, https://usegalaxy.eu/published/workflow?id=d773cbc76253afbf single-cell/EBI-retrieval, single-cell/scrna-case_FilterPlotandExplore_SeuratTools, single-cell/scrna-data-ingest, single-cell/scrna-seurat-pbmc3k
suite_snvphyl_1_2_3 SNVPhyl suite defining all dependencies for SNVPhyl 2015-08-05 To update Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
tables table_pandas_arithmetics, table_pandas_rename_column, table_pandas_rename_columns_regex, table_pandas_transform, table_scipy_interpolate Tools to manipulate and analyze data tables. 2024-11-14 https://github.com/RECETOX/galaxytools scipy To update Metabolomics, Statistics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/tables https://github.com/RECETOX/galaxytools/tree/master/tools/tables 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files 2021-05-05 http://artbio.fr 0.6.1 pigz To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
terrabyte_ogc_api_processes terrabyte_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from terrabyte (https://docs.terrabyte.lrz.de/). 2024-11-11 https://github.com/AquaINFRA/galaxy 0.1.0 r-base To update Ecology ecology https://github.com/AquaINFRA/tools-ecology/tree/terrabyte_ogc_api_process https://github.com/galaxyecology/tools-ecology/tree/master/tools/terrabyte_ogc_api_processes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 10 10 0 0 0 0 0 0 0 0 0 0 0 0 1 3 10 30
thermo_raw_file_converter thermo_raw_file_converter Thermo RAW file converter 2018-09-14 https://github.com/compomics/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.5 To update Proteomics Conversion, Filtering, Peak detection Conversion, Filtering, Peak detection Proteomics, Proteomics experiment, Metabolomics Proteomics, Proteomics experiment, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser ThermoRawFileParser ThermoRawFileParser Open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 91 129 2498 3030 0 0 0 0 20 20 1183 1183 0 0 0 0 111 371 3681 11575 https://usegalaxy.eu/published/workflow?id=3086366b744e8da9
topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. 2021-12-23 https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 13 13 63 63 9 9 25 25 0 0 0 0 0 0 0 0 22 66 88 264 https://usegalaxy.eu/published/workflow?id=2a1b21d39ebb6e49, https://usegalaxy.eu/published/workflow?id=3729015f676693c8, https://usegalaxy.eu/published/workflow?id=bf99d06567288766, https://usegalaxy.eu/published/workflow?id=d4d8e907e26c8587, https://workflowhub.eu/workflows/761?version=1, https://workflowhub.eu/workflows/762?version=1, https://workflowhub.eu/workflows/763?version=1, https://workflowhub.eu/workflows/764?version=1
translate_bed translate_bed Translate BED transcript CDS or cDNA in 3 frames 2018-01-14 http://rest.ensembl.org/ 0.1.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 141 146 606 707 109 109 481 481 19 19 889 889 0 0 0 0 269 812 1976 6029 https://dev.workflowhub.eu/workflows/1042?version=1, https://dev.workflowhub.eu/workflows/1201?version=2, https://dev.workflowhub.eu/workflows/1386?version=1, https://dev.workflowhub.eu/workflows/1398?version=1, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474 proteomics/neoantigen-2-non-reference-database-generation, proteomics/proteogenomics-dbcreation
translate_bed_sequences translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column 2016-01-13 0.2.0 biopython 1.70 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16 21 50 69 0 0 0 0 0 0 0 0 0 0 0 0 16 53 50 169
ucsc_cell_browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets 2018-09-11 https://cells.ucsc.edu/ 1.0.0+galaxy1 ucsc-cell-browser 1.2.15 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 172 183 915 982 0 0 0 0 0 0 0 0 0 0 0 0 172 527 915 2812 https://usegalaxy.eu/published/workflow?id=5d31bafd82547d5d, https://usegalaxy.eu/published/workflow?id=71f7725b261c6c83, https://usegalaxy.eu/published/workflow?id=ebfd7cabc0dc97f8, https://usegalaxy.eu/published/workflow?id=f27abf3c623d3062
unipept unipept Unipept retrieves metaproteomics information 2015-04-03 https://github.com/galaxyproteomics/tools-galaxyp 6.2.4+galaxy0 python To update Proteomics Prediction and recognition, Visualisation Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows Proteomics, Proteogenomics, Biodiversity, Workflows galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 267 283 5231 5595 92 92 289 289 31 31 1199 1199 0 0 0 0 390 1186 6719 20521 https://dev.workflowhub.eu/workflows/1041?version=1, https://dev.workflowhub.eu/workflows/1159?version=2, https://dev.workflowhub.eu/workflows/1177?version=2, https://dev.workflowhub.eu/workflows/1338?version=1, https://dev.workflowhub.eu/workflows/1352?version=1, https://dev.workflowhub.eu/workflows/1371?version=1, https://usegalaxy.eu/published/workflow?id=00e246ea459b0991, https://usegalaxy.eu/published/workflow?id=02700454f57eb556, https://usegalaxy.eu/published/workflow?id=0e0be913c3e27022, https://usegalaxy.eu/published/workflow?id=1706bfa819bbfa89, https://usegalaxy.eu/published/workflow?id=17a1433d0b681d4a, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=28af61ead68e0976, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=58db3e1996a8f093, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6766bed39f614b7c, https://usegalaxy.eu/published/workflow?id=68967c922de149ae, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6da171871d4f3fd5, https://usegalaxy.eu/published/workflow?id=755ede37d94dc456, https://usegalaxy.eu/published/workflow?id=78e1769f1dcb797b, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=8f3cafa3bc59ff82, https://usegalaxy.eu/published/workflow?id=8fc1ea9e94bc723d, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=a4d6b9dc6b396933, https://usegalaxy.eu/published/workflow?id=a657b412b37b971b, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=bfe26679d670bb5e, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=d148459a4d4b91f1, https://usegalaxy.eu/published/workflow?id=d9e7a940b2d410bc, https://usegalaxy.eu/published/workflow?id=df926c5ab8d27192, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://usegalaxy.org.au/published/workflow?id=050a66ff6d4c2b53, https://usegalaxy.org.au/published/workflow?id=f9f685d6150e48c5, https://usegalaxy.org/published/workflow?id=3f797bfb67130883, https://workflowhub.eu/workflows/1219?version=1 microbiome/clinical-mp-5-data-interpretation, proteomics/clinical-mp-5-data-interpretation, proteomics/metaproteomics, proteomics/metaquantome-data-creation
uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format 2016-03-08 https://www.uniprot.org/help/programmatic_access 2.5.0 requests To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 244 289 1548 1714 7 7 15 15 38 38 902 902 0 0 0 0 289 912 2465 7561 https://dev.workflowhub.eu/workflows/1351?version=1, https://dev.workflowhub.eu/workflows/1372?version=1, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=5374daf356516a40, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=73dc2384535bf6af, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=cb9a26ea53ce7a27, https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d, https://usegalaxy.eu/published/workflow?id=eeb6cff210cac091, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 microbiome/clinical-mp-1-database-generation, microbiome/clinical-mp-3-verification, proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-3-verification
upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server 2022-01-18 0.0.5 omero-py 5.11.1 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
validate_fasta_database validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. 2017-09-14 0.1.5 validate-fasta-database 1.0 To update Fasta Manipulation, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 49 49 155 155 18 18 42 42 3 3 57 57 0 0 0 0 70 210 254 762 https://dev.workflowhub.eu/workflows/1384?version=1, https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85, https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e proteomics/neoantigen-3-fragpipe-discovery
varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. 2022-11-28 http://artbio.fr 0.1 python To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls 2016-01-20 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
verify_map verify_map Checks the mapping quality of all BAM(s) 2015-05-15 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
vibrant vibrant Virus Identification By iteRative ANnoTation 2024-09-11 https://github.com/AnantharamanLab/VIBRANT 1.2.1 vibrant 1.2.1 Up-to-date Metagenomics Sequence trimming, Scaffolding, Genome annotation Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant VIBRANT VIBRANT Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 19 19 0 0 0 0 0 0 0 0 0 0 0 0 4 12 19 57
vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. 2019-03-13 https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro 0.1.1 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 753 775 15033 15636 0 0 0 0 0 0 0 0 0 0 0 0 753 2281 15033 45702 https://usegalaxy.eu/published/workflow?id=596b073ab7249aa2, https://usegalaxy.eu/published/workflow?id=c0888e0a0fb53ed3
virsorter virsorter VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. 2024-06-20 https://github.com/jiarong/VirSorter2/ 2.2.4 virsorter 2.2.4 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter virsorter virsorter Identify DNA and RNA virus sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 34 344 344 0 0 0 0 0 0 0 0 0 0 0 0 34 102 344 1032
vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations 2019-10-24 https://www.ks.uiuc.edu/Research/vmd/ To update Computational chemistry chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
waveica waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. 2021-02-10 https://github.com/RECETOX/WaveICA 0.2.0 r-recetox-waveica 0.2.0 Up-to-date Metabolomics Standardisation and normalisation Standardisation and normalisation Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica https://github.com/RECETOX/galaxytools/tree/master/tools/waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 53 53 4 4 5 5 1 1 228 228 3 3 12 12 16 48 298 894 https://usegalaxy.eu/published/workflow?id=3086366b744e8da9 metabolomics/gc_ms_with_xcms
wisecondorx wisecondorx_npz_converter, wisecondorx_predict, wisecondorx_reference_builder WisecondorX 2024-12-15 https://github.com/CenterForMedicalGeneticsGhent/WisecondorX/tree/master 1.2.9 wisecondorx 1.2.9 Up-to-date Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/wisecondorx https://github.com/ARTbio/tools-artbio/tree/main/tools/wisecondorx 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. 2020-05-06 http://xarray.pydata.org 2022.3.0 xarray To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 5 2 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 0 284 284 6034 6034 26 26 71 71 3 3 358 358 8 8 18 18 321 963 6481 19443 https://dev.workflowhub.eu/workflows/1185?version=2, https://dev.workflowhub.eu/workflows/1193?version=1, https://dev.workflowhub.eu/workflows/1195?version=2, https://dev.workflowhub.eu/workflows/1260?version=1, https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=4f0f3b911b4e4921, https://usegalaxy.eu/published/workflow?id=6afc245029ce5008, https://usegalaxy.eu/published/workflow?id=6df53b44018b2235, https://usegalaxy.eu/published/workflow?id=7b50e72deb46c6e8, https://usegalaxy.eu/published/workflow?id=a80f9b926ba43892, https://usegalaxy.eu/published/workflow?id=b4bfcbf8acee9cc3, https://usegalaxy.eu/published/workflow?id=d94460f342b70eb3, https://usegalaxy.eu/published/workflow?id=f774cf05ddff3612, https://usegalaxy.eu/published/workflow?id=fc33ea1679e5f1b7 climate/argo_pangeo, climate/fates, climate/pangeo, ecology/x-array-map-plot
xlsx2tsv xlsx2tsv Convert an xlsx file to a tabular 2024-12-16 https://github.com/Helmholtz-UFZ/galaxy-tools 0.1.0+galaxy0 pandas To update Text Manipulation ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/xls2tsv https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/xls2tsv 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
xmlstarlet xmlstarlet Tool to convert a xml file from one metadata standard to another 2021-10-18 1.6.1 xmlstarlet To update Convert Formats ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 100 100 0 0 0 0 0 0 0 0 3 3 3 3 21 63 103 309 https://usegalaxy.eu/published/workflow?id=8a81615501be20fd, https://usegalaxy.eu/published/workflow?id=f98560da584d5abf
xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing 2021-05-26 https://github.com/GoekeLab/xpore 2.1+galaxy0 xpore 2.1 To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
xtb_molecular_optimization xtb_molecular_optimization Performs semiempirical molecular optimization. 2023-08-24 https://github.com/grimme-lab/xtb 6.6.1 xtb To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 185 185 0 0 0 0 2 2 77 77 0 0 0 0 8 24 262 786 https://dev.workflowhub.eu/workflows/1367?version=1, https://usegalaxy.eu/published/workflow?id=4e9a2e12467bc02e, https://usegalaxy.eu/published/workflow?id=5465916d9b51f411, https://workflowhub.eu/workflows/897?version=2 metabolomics/qcxms-predictions
yac_clipper yac Clips 3' adapters for small RNA sequencing reads. 2015-06-17 http://artbio.fr 2.5.1 python To update RNA, Fastq Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
zeiss_lmd_converter ZeissLMDconverter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems 2024-06-29 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 2.0.4 shapely To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 8 8 0 0 0 0 0 0 0 0 0 0 0 0 2 6 8 24
zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. 2024-05-03 https://github.com/AquaINFRA/galaxy 0.1.0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 26 26 0 0 0 0 0 0 0 0 0 0 0 0 4 12 26 78 https://usegalaxy.eu/published/workflow?id=e95bfab07fdec632